Well, the Jihad Hot Spots books pretty much carry the "spine" of the story. I think "Shadows of Faith" was intended to serve as a "main" bit of lead-in Jihad fiction, but that was never completed, nor was "Black Mist Rising" which probably would have delved deeper into the Black Dragon society.
In terms of Jihad fiction, chronologically (starting from the end of the 2nd Star League), we have:
3067-12-06 - Thirteen - Tharkad (Lyran irregulars/reservists mobilize to fight the Blakist invaders)
3067-12-09 - The Last Day of Zeta - Mars (Zeta Battalion's strike on Mars fails)
3068-01-03 - The Line - Luthien (The Black Dragon uprising hits Luthien)
3068-01-06 - Eye of the Beholder - Luthien (Blakists throw themselves into the fracas on the Black Pearl)
3068-02-04 - Dog Soldiers - Part 3-4 - Nanking (Blakists hit AFFS troops on Nanking)
3068-02-06 - Convergence at Khon Kaen (The Chaos Irregulars hunt pirates in the Lyran outback, then are recruited into Uncle Chandy's anti-Blakist coalition)
3068-03-05 - Bloody Dividends - Emris IV (Uncle Chandy utilizes corporate intrigue to interfere with Blakist interests in IrTech and StarCorp)
3068-03-12 - By the Sword - Terra (Case White gets underway)
3068-03-12 - The Breaking of Chemical Bonds - Terra (Case White begins to go awry as the ComGuard fleet is sabotaged)
3068-03-13 - Alpha - Terra (Case White landings begin)
3068-03-13 - The Shade of an Old Oak Tree - Terra (Case White continues)
3068-03-13 - Office Politics - Terra (As Case White progresses, many on Terra express divided loyalties)
3068-03-13 - A Loyal Son of Terra - Terra (A Terra-native ComGuard warrior returns home with Case White)
3068-03-13 - Voice of the Resistance - Terra (Anti-Blakist resistance cells mobilize to support the ComGuard)
3068-03-13 - Stars in the Time of Dreaming - Terra (Case White continues)
3068-03-14 - The Loyal Son - Terra (Raul Tinker fights for the Word of Blake to defend Terra)
3068-03-14 - To Serve and Protect - Terra (TerraSec forces fight to support the Blakists)
3068-03-15 - A Smaller Sacrifice - Terra (ComStar's Texas LZ is overrun)
3068-03-15 - Backroads at Night - Terra (Case White's European theater)
3068-03-17 - The Good Fight - Terra (Heavy fighting around ComStar's Latvian LZ)
3068-03-17 - Omega - Terra (Case White ends in failure - the Blakists retain Terra)
3068-05-08 - Other Perspectives (Historian Bertram Habeas gets personally involved in the Jihad)
3068-06-21 - Just Another Day at the Office - Preston (Lyran forces invade the Free Worlds League)
3068-06-23 - Stalking the Legends - Solaris VII (Solaris VII's arena gladiators unify to fight the Blakists)
3068-06-28 - Janshi - Jonathan (Capellan militia fights to repel House Davion's Operation SOVEREIGN JUSTICE)
3068-07-05 - Toil and Trouble - Sorunda (Lennox's Light Horse discovers Blakists machinations in the FWL)
3068-07-11 - Crucible at Campoleone (The Chaos Irregulars foil a Blakist plot and earn their ire)
3068-08-04 - Expediency - Chagos (Blakists use a disinformation campaign to seize power and neutralize Chagos' militia)
3068-08-09 - The Promise - Chichibu (An AFFS strike team attempts to liberate POWs from a Combine labor camp)
3068-08-13 - Desperate Measures (Raul Tinker rises in the Blakist hierarchy)
3068-09-10 - Arcadia - Morningstar (The LAAF garrison battles raiders on Arcadia)
3068-09-11 - Arcadia - Crescent Moon (Part Two of the Arcadia story)
3068-10-04 - The Shaded Light - Terra (A Blakist merc on Terra begins to question what kind of people he's working for)
3068-10-07 - The Hunted - Thorin (The New Hessen Irregulars battle the WoB 6th Division)
3068-10-12 - The Dragon of Caph - Caph (A lone Clan Warrior preys on Blakists)
3068-10-17 - Seventeen Minutes - Canopus IV (The Blakists launch their assault against the Magistracy of Canopus)
3068-10-25 - The Unkindest Cut of All - Orestes (ComStar's Primus is assassinated)
3068-12-01 - Rehab - Anywhere (Jade Falcons field new ProtoMechs against unfamilar attackers)
3069-01-01 - A Different Hope - Black Earth (The Black Earth Militia and Blue Star Irregulars fight to defend against the Jade Falcons)
3069-01-20 - All the Guts, None of the Glory - Hsien (Blakists fight raiders on Hsien)
3069-03-02 - Color of Authority - Demeter (Worlds in the Blakist Protectorate aren't spared unrest during the early Jihad)
3069-05-18 - Guardians - New Home (Avanti's Angels extract a VIP from the Blakist Protectorate)
3069-06-12 - Fallen Idols - Graceland (Jade Falcons hammer the Kell Hounds)
3069-06-30 - Blue Waters - Part 1 - Monthey (The Periphery Star Guard guards an Interstellar Expeditions dig site)
3069-07-02 - Blue Waters - Part 2 - Monthey (The Periphery Star Guard fends off raiders and gets recruited into Uncle Chandy's coalition)
3069-07-13 - Twisting in the Vacuum (The Star Seeds take an anti-Blakist contract)
3069-08-09 - The Shrouded Blade - Atreus (The false "Thomas Marik" is exposed and deposed)
3069-09-15 - Wolf on the Mountain - Orkney (Wolves and Jade Falcons face off)
3069-10-12 - Negotiation - Arboris (Precentor Gazazel engages in 5th Element-style terrorist negotiations)
3069-10-12 - The Day After (Stacy Church is tasked with re-establishing the Black Widow Company)
3069-10-19 - Face in the Viewport - Marshall (Jade Falcon Freeborn MechWarrior Horse battles for survival)
3069-10-27 - Night Terrors - Outreach (Elson Novacat leads a Dragoon resistance group against Blakist forces)
3069-11-02 - Paying Dues - Liao (Hell's Black Aces fight the Blakists under the banner of House Liao)
3069-12-09 - Demon Star (McKinnon's Raiders is recruited into Uncle Chandy's coalition)
3070-01-09 - Blood Price - Solaris VII (The Solaris Home Defense League continues to battle the Blakists)
3070-01-10 - Dulce et Decorum Est - Terra (The Opacus Venatori get their marching orders)
3070-01-22 - Samadh - Outreach (Stacy Church prepares to lead the Black Widow Company into the Blake Protectorate)
3070-05-01 - Groundpounder - Risin (The Snow Ravens assist the Outworlders in battling pirates)
3070-12-22 - Hunter of the Yellow Bird - Luthien (The battle between the Black Dragons and Loyalists continues)
3071-01-13 - Eisenjager - Tharkad (Lyran armor crews battle Blakist occupiers around the ruins of Semier DataTron)
3071-02-02 - End of Message - Renown (Capellan special forces move against a Blakist HPG station)
3071-02-03 - Whatever the Mess You Are, You're Mine - Niops V (The Black Heart Roses battle Marian raiders)
3071-02-12 - Meiyo - Solaris VII (Blakists hold rigged gladiatorial contests to execute captured Solaris Home Defense League gladiators)
3071-03-14 - Boom - Marantha (Ebon Magistrate commandos strike at Blakist occupation forces in the Magistracy of Canopus)
3071-05-14 - Meet the Players; Orchestral - Great X (Lyran and Jade Falcon forces clash)
3071-05-22 - From the Highest Spire - Part 1 (Kali Liao's cyber-thuggees raid Chesterton)
3071-06-13 - The Frost Advances (The Ice Hellions launch their invasion of the Inner Sphere)
3071-08-25 - From the Highest Spire - Parts 2-5 (Rabid Foxes launch a retaliatory raid against Kali's command bunker on Highspire)
3071-09-13 - Evacuation - Wei (Capellan and Blakist special forces vie for control of a high-ranking captive as Blakist staff tries to flee the HPG compound)
3071-10-02 - The Winds of Spring (The Ice Hellions are crushed and forced to flee the Inner Sphere)
3071-11-05 - The Master's Hand - Gibson (Anti-Blakist resistance forces on Gibson are slaughtered)
3071-11-06 – Defiant Stand (Raul Tinker commands Blakist forces on Robinson)
3071-11-21 - Into the Fire - Bromhead (The Taurian Concordat invades the Federated Suns)
3071-12-04 - Way of the Warrior - Strana Mechty (Clan Wolf says farewell to the Clan Homeworlds)
3072-01-11 - Jungle Warfare - Tharkad (Coalition forces battle Blakists on Tharkad's Tatyana island chain)
3072-02-02 - With Carrion Men - Part 1 - Fanandir (Aris Sung's relief mission to the Magistracy goes awry)
3072-02-16 - A Living Epitaph - Niles (Hell's Horses sibcadets battle Cloud Cobra extermination teams)
3072-03-11 - Just Business - Dalton (The Bounty Hunter matches wits with Precentor Berith)
3072-03-28 - Last Man Standing - Buenos Aires (Blakist bioweapons cause mass casualties)
3072-05-03 - With Carrion Men - Part 2 - Fanandir (House Hiritsu sends a team to find the missing Aris Sung)
3072-07-21 - Eclipse - Ruchbah (The Crescent Hawks hit the Protectorate Militia to liberate POWs from a re-education camp)
3072-07-28 - With Carrion Men - Part 3 - Fanandir (The Blakists have rebuilt Aris Sung as a Manei Domini)
3072-08-13 - Three Sides to Every Story - Gibson (Dueling propaganda broadcasts show different perspectives on the abortive Regulan raid on Gibson)
3072-11-15 - The Few, The Lucky - Galatea (The Last Knights flee Blakist pursuers on occupied Galatea)
3072-11-29 - Isle of the Blessed - New Avalon (A 13-part serial chronicling the climactic Third Battle of New Avalon)
3073 - Found and Lost (A mysterious figure in a hospital claims to be from Jardine, then vanishes)
3073-05-03 - Teach the Wicked - Hall (The Blakists shatter the Martian Cuirassiers and send the survivors to re-education camps)
3073-06-12 - The Fading Call of Glory - Tukayyid (Ghost Bear Richard Bekker fights a Trial of Position on Tukayyid and meets Devlin Stone)
3073-10-11 - Well Met the Future - Tukayyid (David Lear introduces Devlin Stone to Victor Steiner-Davion)
3073-12-08 - Marauder - Warren (A glory seeking AFFS MechWarrior in a backwater posting bonds with a haunted BattleMech)
3074-03-07 - The Walking Dead - Radstadt (Ghost Bear forces fight on after taking lethal radiation from a Blakist nuke)
3074-07-21 - Kindred Soul - Warren (At the helm of the haunted 'Mech, Kevin Langstrom turns to the dark side)
3075-03-17 - Sons of Janus - Blantleff (Mercenaries get in the thick of the fighting between Marian, Circinian and Blakist forces)
3076-04-04 - Sins of the Father - Regulus (After the disastrous Regulan raid on Gibson, Apollyon comes to Regulus to intimidate Titus Cameron-Jones)
3076-06-05 - The Fires of Hell (A mercenary team hits Rochelle to neutralize a Blakist space defense system prior to the arrival of an invasion fleet)
3077-01-04 - Purification of the Damned - Ciotat (A Manei Domini operative purges data from the Star Corps Dossiers)
3077-10-25 - When Small Men Stand - Pacifica (Blakist die-hards battle with Coalition garrison forces on liberated Pacifica)
3078-08-13 - Lyran Fire - Terra (Lyran forces fight a hopeless battle against encircling Blakist forces in North America)
3078-08-13 - The Blood of Man - Terra (TerraSec forces fight to hold back the Coalition in the British Isles)
3078-10-08 - The Bitter Harvest - Terra (Infantry clash amid brutal street fighting in Budapest)
3078-10-09 - Those Who Stand High - Terra (Coalition forces try to stop a Blakist column heading for the safety of a Castle Brian in Colorado)
3078-12-15 - Misplaced Childhood - Terra (Coalition forces engage the Blakists in Wyoming)
3081-04-02 - Vindication in the Ashes - Circinus IV (Hallelujah! It's raining nukes!)
And that's (barring any I may have missed along the way) the extent of the stories we have for the Jihad. Enjoy!
