I need some help

Are you refering to the AMT/Ertl kit with the lift-off trunk? I've built this one in the past, and I have attached the front and rear panels to the body before in stalling the chassis- If I recall, I had to trim the chassis a bit, but the 'surgery' did not show up once the car was together.

What color is your exterior? Try to get a color that compliments it. Also dont forget to paint the interior of the body. Sounds stupid to suggest that but Ive done it myself. You get so focused on the exterior that you overlook it

I'll give it a try.

Leme get you guys opinion, what is a good color for the interior of a car, not like the seats but the floor and inner doors and such

SmeagolI have the same kit at home. My process for it is paint and detail the interior, engine compartment, etc... Install the glass and mask everything from the inside. Fix chassis to body then mask all glass on the outside. Besure your edges are burnished down good. Use paper and anything you can to completely plug openings. Prime. If down a metal flake or pearl paint I like to start with a base of gold for metal flake and silver for pearl. Spray light even coats and build up gradually. spray away from any openings or glass to be safe. After proper drying time use CA to attach any lights, bumbers, etc....

Im going to try and paint the chassis and get all of that finished, and after that is done I am going to mask the inside of the empty wndoes from the inside then put them together.
Since I can not get all of the windows inside I am going to keep the front two windows out as if they were rolled down.

No no, its more then tight.

The front section and the back section where all the lights and such go are seperate pieces.  There not snap and there are no guides and unless the chassis is installed it bends In way to far for it to work, and once they are on the chassis can not be taken out.

I always paint the body and chassis seperatly then put them together, but this one doesnt seem to allow it

The tight fit of the body is normal, actually and not necessarily an indication of warping.

I build cars all the time and paint the body off the chassis and before the glass goes in. I use white glue to install the glass. What is it that you plan on painting that would require masking?

The only things I do after the body and chassis come together is the final decals and any small bits that would get busted off during assembly.

oh, and it cant be completed before the chassis is on because the body is lightly warped and bends in and only the chasis will hold it open so the pieces fit right.

Basically, you cant completly assemble the body until the Chassis is complete and installed in the body.

therefor you cant install the windows after you install the chasis and I dunno how to go about painting this car body when the windows are installed.  and if I can manage to install them after im not sure how to go about masking it once its complete...

Hmmm, well your problem has me a little confused as well. Are you concerned that your airbrushing will paint areas of the interior that are obviously not meant to be touched with the airbrush? I guess I can't visualize the issue as I would assume this could be handled with careful masking and steady airbrushing. When I completed my car, I attached the chassis and body prior to finishing and ensured leaving the interior untouched by masking the windows and stuffing the interior with tissue paper and masking tape.

Sorry if I didn't really help, I'm just trying to understand the situation a bit better.