I hate to say it but it would have been easiest if you placed the headers into the engine compartment while you were installing the engine. After the engine is then secured the headers could be bolted right up without fighting for clearance. Since the engine is already in, your best bet is to raise the car as high as possible and install them from underneath (depending on the brand of headers). For the drivers side headers, you will most likely have to remove the center link to gain enough clearance, and most headers (except TTI) have one tube going under the center link. Good luck and just take your time with the installation.
As for gaskets, just use a good gasket (copper laminated if possible) and torque the bolts down evenly, being sure not to overtighten them which will result in bent flanges and leaks. I have used hi temp RTV to seal header flanges and collectors in the past, but they almost always start to leak some time later after the RTV burns away or detererates.
- Cuda72