A manual tranny '88 would have an ECU (the tech probably just is using the "new vernacular" incorrectly) - The ECU is located directly above your gas-pedal foot's shin behind the dash/kick panel for those years ('87-'90).
Reading liberally you can probably give the tech the beneifit of the doubt that he's talking about the harness running to whatever controls the engine... (he say PCM cause he's new, "ECU" would be more correct).
Before you go getting all excited that this will be major $$$ - look at the large wiring harness in the area above your brake booster under the hood. Your '87 and possibly this '88 (depending on build date) may have a rectangular connector there (C101) - most of the engine sensors and control signals pass through that connector - unfortunately, that connector is notoriously unreliable offering many different kinds of problems - some folks will have good luck cleaning and re-greasing that connector and leaving it in the harness, others cut it out and splice wire to wire (the connector was eliminated from later production) --
Also look at your CPS connector and follow it's wires - they should not go into the main harness, but instead should pass, on their own, through the firewall to the ECU (the CPS re-wiring was one of the first TSBs issued against the engine harness for the RenixII harness - essentially a symptom of the issues with C101).
There are many things that the "new" Jeep techs aren't familiar with (I'd place $$ that he didn't look at the fuses - since the manual tranny's clutch master cylinder tends to fail and leak on the fuse block - a bunch of half-melted connections in the fuse block will cause no end of "issues" as well!)
anyway --
to answer directly -- your '88 XJ has an "ECU" (Renix II to be exact - it's located above your gas pedal foot's shin), not a PCM
(BTW, if you find a computer under the back seat you have/had ABS!)
