Snake,
an 1/8th is a little small, 1/4 a little big...in between works good.
Sounds like you have the body down right this time..congrats! Don't forget to drill and tap the mounting holes from the inside of the rockers to the frame! Remember...this will allow you to put the body on in exactly the same location.
If the rear "1/4" lines up to the rear door, then it's time to mount the rear plates. IF the gap is a little large just put a jack with a 2x4 under the very rear edge and lift up the rear a little to align.
Do NOT be shocked when the trunk liner is off the frame by an inch or two, this is normal. I then put the plates on the frame and push them up very tight to the body, clamp in place then weld, (You can bolt them if you want) to the frame. Now with the cockpit bolted in, the rear brackets installed, you can remove and replace the body at will and it will re-align perfectly every time.
Now is the time to cut the bumper holes, and roll bar holes if you are using one. You can also mount the trunk lid at this time.
Here's a little something we do to get the door locks to match up perfect. Take your time and cut out the door latch area. Use the Bear Claw as a final pattern. Look "inside" the door latch area. Chances are it is not perfectly flat. This will keep the latch from fitting against the body tight, allowing it to rock. We take a small 2" grinder and grind the excess fiberglass flat and smooth until the latch fits tight against the jamb. Now check the fit of the brace from the frame to the latch. It should, but rarely does, fit perfect with no gaps.
Do NOT try and pull it up tight if there is a gap! You will only succeed in cracking the door jamp. I know it's ugly but you want to do it right..no? Cut the bracket apart, bolt one end to the frame, the other to the latch, re-install the plate you cut out and re-weld in place. Now your door and latching mechanism will work perfectly!
That should keep you busy for awhile.
DV -- 300 Cobras are NOT enough! Are you registered?