First... Battletech in general has a massive amount of history that would be hard to absorb by skimming Sarna.net... This isn't a jab, just merely trying to describe the daunting task you may be undertaking...
As for not finding who the Clans were fighting between 2750-3025, well that is because other then themselves, they weren't fighting anyone else. This is because they did not arrive back into the Inner Sphere until 3049.
If you know the name of each Mech, you can check Sarna.net and it should give you some indication of what faction used it. Unfortunately, older designs (like the Archer) are pretty much used by everyone.
After that, you need to make units. Usually for Inner Sphere, 4 Mechs = Lance, 3 Lances = Company, 3 Companies = Battalion, 3 Battalions = Regiment. Clans on the other hand use a slightly different structure starting with 5 Mechs = Star (and after that I never bothered to learn the structure)...
Once you know which factions you have divided your Mechs up into, I suggest going to
www.camospec.com. This is an official sight that breaks down each unit within a faction and tells you their paint scheme... So say you have a Federated Suns (also sometimes referred to as House Davion) lance of Mechs. Go to CamoSpec and click the "Factions" tab. Then click on the big Sword/Sunburst. Then look at the pictures until you find a scheme you might want to paint... Let's say you choose 1st Capellan Dragoons. Click on that name. And it will describe their paint scheme... If you scroll over the little round icons under the name, they will tell you when the unit was active... You can also go back to Sarna.net and enter the name to read up on the unit to see if it is the kind of unit you want to paint.
Camospec mainly gives you the parade scheme, and will almost say something close to "and uses appropriate camo". This means you could pick some camo choice (jungle, desert, tundra, urban, whatever) and just paint them in that. In Battletech that is an option.
Also, if you are looking for decals to use, the place to go is Fighting Piranha Graphics. I believe this is the official vendor for decals.
Caz