Forgive me, as I am only a back-yard mechanic, and not a XJ Expert.
That said, I wonder if your stock ECM is an improper unit somehow for your upgraded engine, as I had the dickens to find a standby-replacement for my RENIX XJ that would properly match up, (by the OEM numbers), etc. Some had/have different bread board components/circuitry for auto, versus manual, apparently, etc. Could it be that your ECM is stock/stroker confused?
Have you googled around for any stroker hints regards ECM changes, or replacement requirements?
You mentioned cowling air intake mod. Some might have everything hooked up, and/or connected before running tests. Given your general expertise, had you, and your bud only tried to start engine with the air duct, or air cleaner box always connected? If so, check to see if there is a rag stuffed into them.
I really doubt you two have gone to that absolute length, i.e., you all must have tried to start the engine without the air duct connected to the throttle body.., hence disregard my 2 cents worth of crazy things that can happen after a few beers on such a job.