I am in the middle of my most recent career mode play through and it started a bit slow but picked up about 1/3 of the way through. I went the route of trying to get higher reputation pirates and keeping it there. The side benefit to this is in order to do that you are pretty much hanging out territory that is not aligned to any faction, but has plenty of missions that don't generally conflict with any factions in particular. So even if you aren't smart about you are going to develop a decent reputation with the FWL, CC, and LC without trying.
The goal behind allying with the pirates was to obtain cheaper entry point to the Black Market, but also the hope was to obtain cockpit buffs so as not to rely on the FWL store. Whether it was just blind luck or poor RNG, I didn't come across many, if any cockpit mods. I picked up a few Ultra, LBs, and a couple Gauss Rifles (but only 1 ton of ammo :(). What the Black Market did provide was a decent supply of Annihilator parts. The majority of my missions in the first 450 days were nearly all cash. On the occasion the max cash wasn't great I'd drag it down a notch for additional salvage. Around that point and time managed to put together two Marauder 3Rs and a Cyclops. Within 100 days of that the Annhilator joined them. I've had a few missions where the reinforcements got the drop on me and did substantial damage, but never destroyed anything.
I've done the flashpoints exclusively to unlock Raven, Hatchetman, and Bullshark. I'd recommend doing all of those again simply because the loss in rep was inconsequential. I would not recommend doing the last battle against the Black Widow and BH until later in your career. The rep gains you get, while substantial, should be used at a later point when you might be struggling to get out of a rep hole with a faction. Also chose your alliances carefully. Once you ally, you lose all that rep with the pirates. I took my alliance with the FWL to get the cockpits I needed and then dropped them. The plan now is to work up rep with the Lyrans or CC again and then travel to the FS/TC side of the map. The other added benefit to taking the pirates is that it fills up your routes fairly well, so if you are trying to obtain points for most planets flown to, it seems to help you out significantly when you have to fly to out of the way places for rep.
Also, amending my previous conversation about Ultra ACs, a base level Ultra 5 trumps the Ultra 2. When you start adding + for damage though the Ultra 2's range surpasses in the Ultra 5 IMO.
