Grandrubie

Ok so I have a wj that I've had sitting for the past year and finnaly got it in my shop to start tearing into it. I started with tucking the fuel tank by cutting and welding spare tire well and cutting and raising the fuel skid. After that was done I replaced my rear main seal on the 4.0 I did this by removing the transmission I know I didn't have to but made it easyer got all back together and got to start it and it just cranks nothing happens so I lumps the gas and it sputter and eventually starts but then when I let of to let it idle it dies. So what I did was reset the computer by removing and touching the neg battery cable to the pos terminal and starts right up and idles so I'll turn it off and go to start it a 2nd time and it will sputter and then just crank with nothing so I'll cycle a 3rd time and no sputter till I rather pump the gas or crank it forever. No lights coming on I replaced the TPS and then the CPS on the bellhousing did not change anything. Could I have messed up the comp from welding on the backend of the vehicle I removed the battery and most of the important relays and fuses while I was welding.