Here is the deal. Here is my approach.
We don't know what kind of truck you are building. A grocery getter or a hot rod with big torque (for some reason).....or maybe a dragster. Probably not the latter, assume a Daily Driver or Show. A super long wheel base, very heavy 1T panel truck is really not a platform for a hot rod. If you plan on keeping for many years, it sounds like a good project. The resale and number of buyers may not compute very well.
Next, I'm old school. Many guys, including me, have done a motor swap to all kinds of vehicles. We don't have Faro Arms or work at a professional shop or are a pro like Evan. I can see you are trying to be meticulous and preplan everything. You want everyone to tell you all the potential problems, but you already have identified them in basic form. So you are a savvy guy it seems. Each build is a little bit unique and a little bit common. The 1T C channel frame is quite a bit stronger than the 1/2 or 3/4 Frame. So strength is there. I believe you have an open drive shaft already. Your choice, as to what differential and trans to use is depending on your requirements for street/highway performance of truck. The motor is already a given. Curb weight is a given.
Upgrades to better steering and stopping is advisable. Power steering kits for 1/2 or 3/4 should be able to be applied to 1T. Front suspension has donor or aftermarket choices or just stock. Suspension kits available for clip to entire chassis probably available....or stock. A 1T build is rare and may require fabbing and/or modification of kits.
Planning it like a NASA moon shot is one style. The better style is mocking it all up to discover all the good news and identify the challenges. You will need to know where the firewall and trans hump is if the body is off. (with your money you can get a beat up 1/2T cab or front of a cab to use)
. Clearances issues and their fixes are identified by mock up. They can not be identified by forum. As you get stuck, we enjoy helping to solve.
It's a highly technical "Whac-A-Mole" technique.
You already have it all apart, which is good. You have access to measure and blumb bob it and think on it and mock it. You don't need a co-ordinate measuring machine or a 3D solid model. If you delete crossmembers, try to replace at a near location. I like the tubular universal adjustable weld or bolt on aftermarket crossmembers for motor and trans. They are inexpensive, light fabrication involved. Don't sweat the small stuff now, like cooling fans and what tint for windshield.
Don't buy a whole lot of stuff, just get to work. We are ready for a fun project.
Can you supply link to the Chevy 5600 thread?