Sounds like you are in a similar place as I was a few years back when I discovered low compression on the #2 cylinder of my 95 TBI. I went round and round and had parts lists and cost for several different options. I am going to share some of that logic and maybe it will help you.
Stock long block. Quick and effective. Would still have rebuild the throttle body and replaced any sensors that were original. Would not have given me the power bump I was looking for but TBI engines are relatively simple and if maintained very reliable. I also feel these engines do a little better in the low end torque area.
Upgraded 350. New heads/cam. Problem here is that the TBI management system is not forgiving to mods. You can get a tunable ECU or get the components to burn the chips. I figured if I was going to dive into tuning or modifying ECU parameters I would do it on a newer system. There are quite a few aftermarket self tuning throttle body systems, but there is extra cost associated with those.
96+ vortec system. Decent power boost over the TBI. Parts, harness, ECU sourced from junk yard or parts store. For the time and money there was more power to be had. I was not a fan of the spyder injector system and my 99 which has this engine has been a bit troublesome.
96+ Big block. Better injection system (IMO), Lots more toque which would have been good for the towing I was doing. Down side was it was going to be pricey and my gas mileage would have taken a hit. Everything would have been pretty straight forward in terms of a swap and I almost went this direction.
LS Swap. Most power gain (but not torque) Later fuel management system. I ultimately went this route. Cores were available and I rebuilt mine myself with outsourcing the machining. Wiring was time consuming. Tuning was not too bad. I could have bought an aftermarket harness and had the VATS and related turned off by a tuner but at the time I decided my time was better spent than the cash. Probably the only one more expensive than this was the big block. I had a good bit in buying new sensors, coils, headers, brackets, ect. I have realized a slight fuel mileage increase even when towing. I kept everything as stock as possible to minimize the ECU changes. If I had gone with a different cam and a custom tune I could have unlocked a lot more power. I still could. I disagree with the earlier comment on the reliability of an LS swap. If done properly there should not be any reliability issues.
Ultimately what I tell everyone is consider what you want to use the truck for and let that drive your decision. I was looking to gain some power when towing and hoping for a slight mileage increase when not. At the time it was easy to get an LS engine as well.
The fact that you have spare vehicles to drive helps. As you go down this list the time factor increases almost exponentially from a weekend job to a couple of months when you factor in learning wiring, tuning, and waiting on a machine shop.
By your original goals in the first post it sounds like just rebuilding your engine or getting a long block would be a good choice. If you start looking at head and cam upgrades it may be worth considering an LS swap.