just keep measuring all the time, and make sure your reference points are square and unchanging. Every shim, twist, and move you make will affect something else so always be thinking 3 dimensionally, and every 30 minutes stand back as far as you can and take a look at the "squareness", and don't forget to choose new "angles" to look at the car from not just the same place every time. Have several long straight edges and definitely buy a digital level, I use that thing all the time.
I've dropped my body in various states on top of 2 or 3 chassis now and I'm just a dude with a carport. My first time I had the body with no floor and no real bracing stood up on 6-8 cinder blocks while I rolled the completed chassis, roll cage and all, underneath it on furniture dollies. The last one I started with just a roof and a-pillars, so less structure and form than you have. Again I'm just a one man amateur show out in a carport. Give that garage space you have you are a luxurious shop. You can do it !