I drive a '90 with the 258, and my younger brother drives a CJ-7 with the same 258. He is having a similar problem, and the problem is in the plug for the computer. When the jeep is cold, he has to wiggle the plug or he gets no spark whatsoever. Neither of us have done the "infamous" nutter bypass, but we're going to try it next weekend to eliminate the computer and see if that solves the problem (because the ignition module passes through the computer on the way to the cap--we've been kicking around the bypass for both jeeps for a while now). I know this isn't a definitive answer to your problem, but like our situation, it could be something as simple as a wiring connection.
Currently an '86 CJ-7---following a string of '01 Sahara, '90 Sahara, and '85 CJ-7. Finally got back to how it all began....