You may have a variety of problems based upon how the swap was done. Do some basic, common sense checks before you go much further. MAke sure your supply & return fuel lines are flowing freely, no blockages or kinks, etc., and that they are connected properly. If it was originally a V8 CJ, both hard lines from the tank will be on the driver side frame rail. If it was originally a 6 cyl, the supply line is on the passenger side. Make sure you have them connected properly to your FI system, and also be sure they're correct at the tank sending unit. Some guys will reverse them by mistake.
Also, make sure the lines are routed well away from engine heat. Don't run them up over the top of the engine, water pump, etc. I saw one like that a couple weeks ago that stopped dead on a steep mountain trail nearby. I'm not sure what side your EFI's fuel intake line is, but route your line to that cleanly and away from engine heat. If the inlet port is on the left side and your supply hard line is on the right, run the flex line all the way to the front cross member, that is, under the radiator support, then around to the driver side. Do the same with the return.
All that should ensure the lines aren't getting so hot the fuel is boiling. If necessary, insulate the lines with something like foil or glass fiber wrapped in foil, etc.