Not having a cross member in the far rear of the frame isn't all that uncommon. Nothing to worry about there.
It probably couldn't hurt to measure the engine compartment, but it may not be all that important. The cool thing about medium duty and up chassis is that stuff like suspensions, steering box locations, motor mounts and nearly everything else aren't all that hard to move where you need them. The frames on pretty much all these trucks are straight and that makes it so much easier because of not having arches in the frame over the axles and such.
Lets just say that the frame you use has the motor mounts in the perfect place but the steering box mount and suspension won't be right. Usually on these frames, the spring hangers are either bolted or riveted to the frame, usually riveted. It would be easy to cut those rivets, move the mounts where you need them, re-drill the holes and remount them with grade-8 bolts and lock nuts. Pretty much the same thing with the steering box. One thing I can foresee is your new steering box having to be remounted and the steering shaft no longer working because it's the wrong length. Easy fix... Go to Borgeson's website and you can order a custom steering shaft with ends that will adapt your new steering box to your old steering column. I bought one of these steering shafts from Borgeson for one of my projects, and I can't tell you how impressed I was with the quality of their stuff. I didn't know whether to install it or frame it and hang it on my wall!
Not sure what to tell you about the insulation. I never got into the walls in my old bus so I don't know. But as a precaution, you might want to wear some kind of respirator/filter if you're removing it. Back then they didn't know that some of that stuff wasn't good for your lungs.
As far as the spot welds, you're probably going to have to drill them or grind them out and re-weld the holes shut and grind them back flat. No real easy way to get around that.
BTW, post lots of pics when you get them. We all love to see progress pics!