I'm sure that in your rebuild you would have certainly reinstalled the flex plate back on correctly since it can only be reassembled one way . That is of course important in establishing correct ignition timing with the CPS . But it still sounds like an ignition timing problem . Can you verify that the cylinder firing is in fact on TDC compression stroke ? I'm sure you feel that you did correctly plant the distributor back in correctly but please do try to check over your work since the engine isn't starting correctly . Once when I helped a friend install a timing chain and gears on a V6 Buick engine we had correctly installed the distributor correctly. Same results , no start. He disassembled the the front engine cover ( timing chain cover) without indexing the distributor and I had to rescue him. After many attempts to pull the distributor and line up oil pump,drive and finding #1 TDC did we finally get it running. Theoretically , all a distributor has to do is be pointed on #1 terminal and engine on #1 TDC to,run but I have seen many times where correct indexing to be the only way for an engine to start . The 4.0 distributor has no dwell setting for you to manually try to find the right timing mark ( retard and advance) so,it is critical that the distributor be installed correctly. Please do go,over FSM instructions and verify all in compliance . Since the engine is not running , you've got nothing to lose. As long as flex plate is right ( can only bolt up one way due to hole spacing differences on crank hub) and timing chain is to , it falls on distributor placement.