I leaned into the "well, what if my own VM/XA" because, uh, VM/CMS has the odd distinction among IBM's operating systems of the era of being both (1) source available and (2) site-assemblable. I've gone through my fair share of CMS and CP generations, which felt like a more complete rebuild of those nuclei than the MVS sysgens I've done.
That there makes me feel a little less confident in an MVS 3.8j patching effort.
Primarily just intercept SIO/etc instructions, and replace them with the XA equivalent.
Another idea that comes to mind: you could locate the I/O instructions in MVS 3.8J and patch them over with branches to some new "I/O translation" module. The problem I think with that, is while the majority of IO goes through a few central places in the code (IOS invoked via SVC call made by EXCP), there's I/O instructions splattered everywhere in less central parts of the system (VTAM, TCAM, utilities, etc).