I agree, have your body built on your chassis, also if they sell chassis (and most manufacturers do) get it from them. I had a custom stretched 34 perimeter frame built (for blower motor clearence) and its at the body manufacturer right now, the frame manufacturer (very good, he builds for speedway, alloways, P&J's and many others) accidently put the body mount holes measured off the front crossmember, since the frame was stretched it put the body mount holes 6" off, since the body was built to that chassis no issues, the body manufacturer simply made it work, like Shine mentioned if something is off the fingers start pointing.
Not all body manufacturers use a frame with original dimensions, though I would make sure they would interchange if I was shopping for a body, just off my head, the notoriously known Classic Motor Carriages used a piece of junk frame they made to fit only there bodies, I believe the old Zipper cars used a custom frame and several bodies might only fit a "pinched" frame, even speedways Low boy cars are on a custom frame I believe,
As far as suspension parts not matching up, heck these are hot rods, most are not running any stock suspensions or a bunch of custom suspensions are used anyway, some work some don't that's for sure, just do your homework My advice is write down everything in your build before buying anything and build as much on paper as you can, you will need this if you have somebody build a chassis for you, they need to know front & rear suspensions, brakes, motor, tranny, rear end, tire & wheel sizes & even ac or no ac plus many items not mentioned. Above all have fun! Looks like a cool project.