Well, heres my dilema.  I am not sure what to do next.  I have the suspension all on though not torqued since there is no weight on it yet.  Have the brake lines on, am about to order new fuel hard lines.   I am thinking about dropping the body on next and leaving the engine and transmission till last, my theory here being since im doing my own body work it will be very labor intensive as opposed to the drivetrain as more wallet intensive since it will be mostly new parts because I am missing most of them.  So the big question is what else should I be doing before the body goes back on?

Patting yourself on the back for a job well done?
While it would really be best to install the drivetrain before the body drop, ya gotta do it it which-ever way is good for you and your time/$$.
Brake/fuel/vapor return lines must be installed before the body. Fuel tank would be easiest now, also.
Really sounds like ya got it all under control, Matt.

I'm with Adam on the body drop. So much easier to do drive train before it goes on. You can do all your body work while it's off the frame as long as you are properly supported. One advantage to that is your frame stays lookin' sharp. I even painted mine on the dolly before it went on the frame.

It really is lookin' good!

Im just concerned that when I put the body back on the frame, my door gaps, and hood lines will all be different, also since I want to permenately glass the front bumper on would that be a problem since there are some supports that tie to the frame?

If your gaps were right or even close before you took the body off, then you shim the car on the dolly to make them fit like they did on the car. I hope you remembered to count the shims at the body mounts when you pulled the body. If so, all you should need to do is put the same number of shims back. When you are glassing in the front bumper, be sure to put your hood on, movement at the front will affect how the hood fits. I did all my heavy body work on mine before the body came off, made sure everything fit like I wanted to.

I'm looking at your picture, that's not a brake line running by your carrier and strut rods is it?

well, I didn't keep track of the shims, but I dont think it really matters anyways since most of the body mounts had to be replaced and that would change the number of shims needed anyways.  Also, I have no idea how the doors fit before the body came off the frame since they were already off when I got the car.  One of the many difficulties of buying someones project they couldnt finish.

I think what your seeing as a brake line is the heat shield for the fiberglass monoleaf.

Thanks for the advice and Im open to any more suggestions

You can still do a lot of body work on the dolly. Since you're going to have to re-shim, just start with the pass. compartment, get it stable and level. Firewall mounts, sill mounts and the mounts forward of the rear wheels. If your sill plates are good that will give you a starting point to hang your doors and fit the nose and rear section to it.

What's remaining for you to do on the body?

I have pretty much everything to do on the body other than dissasembly, I havent touched It since I bought the car

If it needs to be stripped, I'd definitely do that off-frame. If you are concerened about fit after setting the body back on, then concentrate on individual panels. If you have the doors that came on the car to start with, that will help with fit, sometimes repalcement doors can be a pain.