Update: Problem solved (fingers crossed).
Problem 1: Backfire through intake on acceleration under load.
Solution: Pulled the fuel tank drain plug (on the 1968 FJ40 it is an M12-1.50 Pitch bolt) went to NAPA and they had a oil drain plug that is the same pitch and perfect length and, best of all, has a hole already drilled part way through it. I bored out the rest of the new drain bolt and made the existing hole in it a little wider, I also added two cross holes in the shaft of the drain bolt because the drain threads in the Cruiser tank have two holes in them to drain the gas in the bottom of the tank (I don't know if this was necessary, but if you do this, make sure you properly clock your bolt with the gaskets installed so the holes end up in the right place). Then I took an 90* elbow section of hard fuel line from a TBI chevy and welded it inside a nut of the same diameter as the drain plug bolt (17mm). Then welded the two together. Plan two for this was to weld an AN-6 bung onto the drain plug, but I got impatient. The result is ugly, and I had to pull the tank to put it in (because the frame got in the way of spinning the plug in) but it is functional and stout. I still need to armor the lines with some frame sliders, but no more backfire (at least as of the last 2 test drives).
Problem 2: Overheating.
Solution: Don't be an idiot like me, use a fan that matches the rotation of your belt. When I switched to the 95 K2500 350 one of the reasons was because I wanted a serpentine belt. I didn't realize that it spins the opposite way from my old v-belt. You might realize this is your problem when hot air is being blown at you when you set your timing standing in front of the engine.
Problem 3: Hard start when engine warm.
Solution: This one was pretty confusing. After driving, if I stopped the cruiser (gas station etc) when I tried to start again it would crank and crank, but not start. Needless to say this was totally lame. I would run my battery dead trying to start. In the end, I swapped out my starter motor, which didn't make sense to me, but it is starting fine now. If you are wondering, I don't have headers and my rams horn exhaust on the starter side doesn't go near the starter. I don't get it, but it worked.
Thank you all for your help. I really appreciate it as you got me through a pretty frustrating time where I actually considered just selling the Cruiser (gasp). Thanks for walking me back from the edge.