Left key on three days, after jump starting it, it runs rough and misfires?

I've pretty much done all that and rerouted some injector wires that were stretched around a coil pack. It runs pretty good when cold but not so good when warm. I hooked it to my boat and went to the lake. It misses a lot when its lugged and first give it gas then gets better a bit when stomp on the gas or shut of the overdrive. It does show a code for random misfire, but most misfires are still on #2 cylinder and some on #3. It does show lean on bank #1. I have done every test for vacuum leak and can't find one. Rail pressure is 39 PSI on both sides. Scanner shows EGR and MAF to be okay. As for spark plugs, I called Ford dealership, and they say $800.00 plus, time and material for whatever they break.
It's getting more confusing by the minute!

Well, It's getting better. The injectors look good. It doesn't miss during normal driving but when I hit passing gear or if I lug it in OD it starts missing. Let me give you some numbers and see If you think I may have a week MAF sensor. (752 rpms) LTFT1 4.3% LTFT2 8.5% STFT1 5.22% STFT2 5.75% BARO 147.5hz. I'm at 900' above sea level I was told the BARO should be 160-170 at this altitude.
What do you think?

When I unplug the MAF the engine shuts off but I can restart it with the MAF still unplugged and it seems to run fine. I haven't drove it that way. Anyway, It's running better now and I don't know why. I drove it about 30 miles yesterday and it didn't throw any codes. It still lacks power and bank 1 reads lean on my scanner while engine is running.
It is confusing for sure.

Okay, will do. I forgot to mention I reset the elec throttle relearn. I don't think that has anything to do with why it's running better. Gonna check the fuel mix with MAF off in a bit.

I'm not sure of anything now. The problem started when I left the key on for three days. After checking everything all I've really done is put in some coil pacs-didn't-seem to help. Cleaned the MAF and throttle body-didn't help. Reset PCM-didn't help much. A few other minor things-ran a little better. I loaded the fuel with sea foam hoping it would loosen the plugs. Gradually it was getting a little better. Later today the fuel trims were okay, and I got lean on both banks. It didn't throw a code p0171 or p0174. It was the data stream on my scanner that said lean. This evening it was running pretty good-a little vibration at idle but no noticeable miss while driving. I'm not saying it's fixed but i'll know when I hook my boat to it. I really have no Idea why it's running better unless the sea foam cleaned the injectors, or did it take the PCM that long to relearn everything?
It's been nuts.

Oh, after I plugged the MAF back in it would idle at 8.G/s but when I drove it and punched it the g/s would go up to 880. That way higher than before?

80 g/s not 880.