Check to make sure your CPS sensor is tight.
Whats the story about the fly wheel? Is it from the 96 or the 93 and at any time was it removed? It has a dowel hole to to line up with the crank but I wonder if its possible to have it flipped and still have the tranny mount up to it.
How about the distributor where did it come from? There may be differences from a 96 ot 93. Some say the engine will run but run bad if its one tooth off. I experimented with that and took it one tooth back and forward. It would only idle and soon as I hit the throttle it would die. So maybe check the timing. The manuals dont show this procedure, but if I remember right put the #1 cyl at TDC if the rotor isnt on the #1 plug wire the remove the distributor and put the roter at the 3 oclock position then as it slides back in it will should be inline with the #1 wire on the cap. The slot on the oil pump may need to be moved to get it back in.
2006 Jeep Wrangler X, 4.0 4:11 gears
'90 Cherokee XJ,W/'91 4.0L reman/ 3.5" RE lift, W/31" M/S tires, 4:11 Gears W/Speedo gear change/ Aluminum Coolant Tank
A/C Conversion/Home Built Roof Rack/K&N Box Filter
Derale 15" Rigid Radiator Fan PT# DER-17415, through Summit W/2"X5/8X5/8"" spacer