Heat is ussually the answer for the stubborn ones, but you're right to be careful with it on that truck. I did a '37 D-2 a few years back with the exact same setup, bolts up through the frame rails into wood sills. What worked for me was a small torch tip and heating just the bolt head or nut for maybe twenty or thirty seconds, then hitting it with the breaker bar while it's still hot. You're not trying to get everything glowing, just enough expansion to crack the rust bond in the threads. Keep a spray bottle of water and a fire extinguisher right there, and put a wet rag or a piece of sheet metal between the torch and any wood. The old paint will bubble and stink but that's cosmetic at this point.
If you'd rather not run a torch near the wood at all, try the candle trick. Warm the bolt head with a heat gun if you've got one, then touch paraffin or even a regular candle to the joint and let it wick into the threads as it melts. Works better than most of the store-bought penetrants on seized fasteners. Also, give the ones you've allready soaked another day or two. Penetrating oil needs way more time than a week on fifty-year-old corrosion, and reapplying it helps.
Another thing that saved me: an air hammer with a blunt chisel bit, striking the bolt head square on. The shock alone breaks loose bolts that a breaker bar just twists. If you don't have an air hammer, even a big dead-blow hammer smacking the head a few times before you pull on it makes a difference. On the mounts, don't count on repro parts for a truck that age. Some of the IH suppliers have sheet metal and hardware for the late 30s trucks but body mount plates are hit or miss. Honestly, fabricating new ones is the way to go. The originals are simple flat stock with a hole in them, so trace one intact-ish piece onto new plate steel, cut it, drill it, done. If every last one is rust flakes, measure the bolt spacing and hole diameter off the frame and box and build from there. And before you lift the box off, photograph everything and label the bolt locations. You'll thank yourself when you're putting it back togehter next year.