Most places don't even sell replacement boots because once its torn the CV joint is usually compromised with dirt and needs to be replaced or it will soon fail.
check for 12v at the fuel pump connector with the ignition on.
check engine compression in case you have mechanical issues
how do the spark plugs look?
you can buy a fuel pressure gauge for the fuel filter banjo fitting that would answer most of your questions.
How does the cap and rotor look...
You are under the impression that you bought it brand new from AZ but really what you bought was remanufactured. These reman'd parts - Alts, starters, axles, etc have a high failure rate and many are DOA. I'm not surprised. Just have them replace it under warranty.
I doubt it. Totally different engines. They are different part numbers for a reason. Otherwise they would use the same part number if they were compatible.
There is a release bolt on the banjo fitting of the fuel filter. $10 says you will break it when you retighten it tho. You can loosen any hose connection on the supply side. Its all the same thing. Have a towel ready.
220k is a lot. You have many things that are near failing and you're about to introduce more stress and heat. That's going to push parts to break. Plus $3160 is not enough. That's a tight budget for everything even if you buy ebay garbage parts and then you're guaranteeing more parts will fail...
Its odd that you had to replace two fuel injectors. Its rare that one fails let alone two at once. Makes me think the fuel injector wasnt the initial problem to begin with. Regardless I would have replaced the full set so you are running a matched set. It has nothing to do with OBD0 vs 1 but its...
So they just threw in over sized bearings without the required machine work to run oversized bearings? More than likely the crank is toast and/or not cost effective to repair.