Oh boy, you have a big task ahead of you. Congrats, and before you know it, you'll be buying more ships...
Feds:
The CA, CS, BCH, DNG, all can have issues with the engine pylons being too big to fit into the socket. This assumes the socket is correctly molded, which is not always the case. The POL are the worst I find, requiring much trim and fit work until they sort of go into the socket.
The connection between the saucer and pylon can be dicey, requiring some tweaking. The DNG is the worst offender here.
You will likely want to use some kind of 1-minute epoxy on these models.
Fed FF, CL not as bad, some fitting of the engines to the slots (which also are often mis-molded) in the FF hull is often necessary. The CL seems to be one of the least problematic minis. I usually just use Superglue GEL with these.
Often times the engines are not perfectly aligned, with significant misalignment of the two halves.
Klingons:
I think the wings are the most problematic, because the minis were designed for resin. The ones I had the most issues with were the C7, D7, D6. Sometimes I can get the wings to go on with the Superglue gel, sometimes not. Even if you get the wing/engine to stay on with Superglue gel, they are fragile, and I recommend running a bead of epoxy on the underside of the body where the wing connects to the body.
The D5 hulls seem to be less picky about the fit between the wing and body and while I have had some issues, they seem to be easier to glue. Still a bead of epoxy on the underside of the wing/body connection is a good idea.
As for the C8, I haven't had much luck using nippers or cutting the resin plugs off with an Exacto knife. I suspect a small Exacto saw might do a better job. You will probably want to use some putty on the divots in the hull after you cut off the resin plugs.
I have also found that all the minis benefit from judicious puttying up and smoothing. Spend a lot of time cleaning them up if you can; the final paintjob will be the better for it. Before you putty them up, do yourself a favor and figure out what color the base hull is going to be. I did not think about this with some of my first Fed miniatures, and let me tell you , it's a real pain in the butt trying to cover up green Squadron putty with white paint. White putty under white paint, green putty for Klingons. I used White putty for the Roms as well.
