On going issues with an old Ford 390fe?

could be a timing issue my old ranger back fired found out it was the timing chain and gears also might need fuel pump, might need new spark plug wires, new ignition coil, bad cam, bent or broken push rod and if so get all new ones and new rocker arms plus if u need a cam get all new one too, intake valves might be bad or jammed, Valve spring, a bad gasket on my fairlane made it backfire it was a head gasket, and it might have too much back pressure from the exhaust

Been there and gone through all this with a 1964 Galaxie with a 390 that sat for 5 years. You can make all the changes you want and all the adjustments you want and it will all be in vain until you pull the gas tank and have it completely cleaned, flushed and renewed. You said it in the very beginning that you had water in the tank and that causes rust and in turn you will never get all the water out even if you drain it. It needs to be pulled and cleaned correctly. There are probably all kinds of rust and dirt along with condensation floating around in the tank. Every time it gets low in gas it will pull all those little particles up around the sump and into the fuel filter. So start back at the tank and then work your way forward.

take the box off the fender,take it to autozone or advance (i know for a fact that autozone can) and have them check the box one easy way to tell is if the jell on the bottom of the box is melted down the fender replace it they should be 25-30 dollars,check fuel filter, maybe the timing is too retarded,have you checked timing and im guessing its around a 1975 or so? at the base of the distributor make a markon the dist. and the block then push the dist.clockwise a little bit and see how it does.the way i set mine is get it up to temp and push the dist. around a little at a time and push the throttle all the way open and see how it reacts it should rev without hesitation then get in it and put it in drive and power brake it listen for a rattle if you hear it the its too far advance so back it up a little then do it again till you dont hear it then shut it offsee how it starts if its sluggish its still too far advanced but it starts fine then road test it.i have a 460 thats built up big cam and thats the only way i can set it

as long as it has set it sounds like you may have a valve sticking,one way to check is to raise the idle to say about 2000 rpm and slowly pour transmission fluid into the carb it will smoke like crazy so do it outside and if you live in the city you may want to consider the amount of smoke this will usually solve the problem for some time however if the valve continues to stick it has a scored spot on the valve stem and it will need a rebuild on the heads.

did you change fuel pump

take clear bottle put fuel hose from pump to bottle crank engine over check color of gas if milky or cloudy

may have bad fuel pump or water in diaphragm or hole on fuel line

change fuel pump take a hose put it in new gas in cherry can try that

see how it work