OK I let her sit up for a while.....
When I turn the key the fuel pump doesnt kick in like it usually does.
When I actually try and start the starter turns the engine over but..... no start.
She ran fine the last time I messed with it.
Had to put it in jacks for rearend swap and ended up leaving her on jacks for about 3 months.

Check your fuses first. 

All fuses in tact and functioning properly.
Visual inspection of wiring harness.  No apparent issues found.

Might be a bad fuel pump.  Can you try running 12v to the fuel pump directly and see if it is working?

There is also a way to check your fuel pressure, but I am not sure how on your particular engine.  You could check that as well.

OK I let her sit up for a while.....
When I turn the key the fuel pump doesnt kick in like it usually does.
When I actually try and start the starter turns the engine over but..... no start.
She ran fine the last time I messed with it.
Had to put it in jacks for rearend swap and ended up leaving her on jacks for about 3 months.

Can you hear the fuel pump relay click on and off?  It clicks on right when you turn the key to "on", then it will click off about 3 seconds after the key is turned to the "on" position.  If the relay is clicking on and off, then it is somewhere between the fuel pump relay and the fuel pump (bad wiring, bad fuel pump, bad connection).  If the relay isn't clicking on, then it is somewhere before the relay (wiring, fuse, main relay).  Easiest thing to do is...once you determine if it is before or after the relay....get your test light out and start checking for voltage.

No repay click at all.... no nothing.... It is before relay that is why I was wondering if it could be the computer

No repay click at all.... no nothing.... It is before relay that is why I was wondering if it could be the computer

Could be.  But first, try swapping the main and fuel pump relays (they are both right there together), and see if by chance the fuel pump relay decided to die.  The main relay also feeds voltage to the fuel pump relay.....so you want to make sure you are getting voltage to the fuel pump relay.  If it checks good, then you have to start backtracing the wiring to see where you lost voltage.

Im having the same problem on my 90 samurai,but it'a not getting any spark.I flashed the check engine light and its giving me a code#41 it say's in the description that it has either a bad connection or broken wire in harness.I checked every bit of my engine and dash harness and came up with nothing wrong,when i checked voltage and resistance in my ignition system im only showing 5 volts at my ignition return to the computer.most vehicle's have a 5 volt reference but this is supposed to have a full 12 volts from the battery.to this day i still cant figure out if its the harness somewhere or if its the computer.BUT I CAN TELL YOU IF YOUR RELAY ISNT KICKING ON AND OFF TO PRESSURE UP THE FUEL SYSTEM THAN IT'S MOST LIKELY THE RELAY WENT BAD.ALL YOU HAVE TO DO TO FLASH YOUR CHECK ENGINE LIGHT IS TO PUT YOUR 20 AMP FUSE AT THE VERY BOTTOM RIGHT SLOT IN YOUR FUSE BLOCK AND FLIP THAT LITTLE TOGGLE SWITCH UNDER YOUR DASH ON THE MOUNTING BRACKET FOR YOUR STEARING COLUMN AND DASH SUPPORT.TRY THAT AND SEE IF YOU LIGHT FLASHES A CODE.

Im having the same problem on my 90 samurai,but it'a not getting any spark.I flashed the check engine light and its giving me a code#41 it say's in the description that it has either a bad connection or broken wire in harness.I checked every bit of my engine and dash harness and came up with nothing wrong,when i checked voltage and resistance in my ignition system im only showing 5 volts at my ignition return to the computer.most vehicle's have a 5 volt reference but this is supposed to have a full 12 volts from the battery.to this day i still cant figure out if its the harness somewhere or if its the computer.BUT I CAN TELL YOU IF YOUR RELAY ISNT KICKING ON AND OFF TO PRESSURE UP THE FUEL SYSTEM THAN IT'S MOST LIKELY THE RELAY WENT BAD.ALL YOU HAVE TO DO TO FLASH YOUR CHECK ENGINE LIGHT IS TO PUT YOUR 20 AMP FUSE AT THE VERY BOTTOM RIGHT SLOT IN YOUR FUSE BLOCK AND FLIP THAT LITTLE TOGGLE SWITCH UNDER YOUR DASH ON THE MOUNTING BRACKET FOR YOUR STEARING COLUMN AND DASH SUPPORT.TRY THAT AND SEE IF YOU LIGHT FLASHES A CODE.

Code 41 is a fault in the Ignition Signal Circuit (as it sounds like you know).  So I would guess if the ECM is supposed to be seeing 12V, but is only seeing 5V, that is what it doesn't like and why it is throwing the code.  I'd get a wiring diagram and start testing to see where you drop from 12V down to 5V (first verify that it is supposed to be seeing 12V and not 5V).
And when you test for codes, you don't have to flip the switch under the dash....just put a fuse in the diagnostic place in the fuse block, turn the key to "on" and watch the check engine light to see what code it flashes.

when u did the rear swap did u weld anything or use a torch? sometimes u can fry stuff when u weld my dad did it once to his chevy the computer just fried. and with the torch the heat rising under the truck the wires from the tank might of got hot enough to short