1995 Jeep Wrangler Vehicle Loses acceleration on inclines.

Vehicle ran fine up until recently. I did some checks on it, but daughters BF did the physical work after conferring with me.
Changed fuel filter / checked rail pressure = 20-37psi
variably. Checked fuel pump sock. Found ok / checked and found fuel spray (leak) from supply 90 ° fitting on top flange of pump, and unbelievably shooting back into tank from a dime size hole in the pump mounting flange. Wierd situation. OK
Changed out the pump (new). Fuel pressure 43#psi.
NG. Found vacuum hose from manifold intake broken / replaced / re: Fuel press=33 psi. Good
Run the car to fill up gas. Now engine cranks, won't fire. / Found bad cam position sensor in the distr. / Replaced / started right up. Loses power on acceleration / shifts up / down ok. Reset TV cable adjustment /ok / still loss of power. Engine cold starts on 1 revolution of crank, and idles perfect. No smoke / revs. Up ok in neutral.

DD's BF. Comes over today, and we were talking. He said his buddy thinks the engine needs a rebuild, and he would do it free cause he's done them before.
THEN. BF tells me he needed to borrow the battery for his pickup, and he pulled it out of the jeep, and installed it but found the battery dead. (0) volts. Hmmm? How could the jeep start?

No battery in the jeep (and I almost fell off the porch hearing this). He reached in and turned the ign switch.(Key). And The Jeep STARTED*****
Right then and there, I knew there was something not right. Come to find out. The big amplifier she has in the entire back of the jeep. Was blowing the alternators, and BF replaced two of them within a month. Another Buddy.(A car radio installer) said the way the amp was hooked up, it would spike the alternator and could cause rectifier problems on the alternator. He installed like two 2,000 mfd. Capacitors in parallel with the power circuit supplying the amplifier. So the Jeep was starting on the energy (Weird) stored in the capacitors!/? I don't know, but I would suppose a bleed resistor should be put across the terminals on the Capacitors so they would discharge after power is removed.(Amp shut off)?
Still, the alternator puts out 14.6 volts while running, and with all the other power functions, I would think that there is not enough reserve voltage, or shall I say high enough voltage to supply the ecm and the fuel injectors. I tested firstly the output of the TPS and that was ok. Also I did a resistance (ohms) test with a simpson 260 analog ohmmeter to watch for poor wiper contact on the TPS, and I found it to function perfectly as described.
I didn't do a output (amp) test on the alternator, and that can be done simply. I have a little experience with electricity and voltage, being a retired HVACR mechanic 45 years.
Any Help would surely be appreciated. Maybe a diode inline feeding the voltage to the amplifier so there would be no noise (back emf) from the capacitors.
I mean It's scary watching the engine run, and on the ground there sits the battery, Not Connected to the vehicle.