This looks to finally be sorted out. Got a look at it again just after midnight and it seems to be working as it's supposed to now. For any of the SERG riders that might consider adding the alarm system should yours not work the problem here was at the connector that originally went to the TSM in front of the battery.
I could have screwed it up. Well within my capability. So double checked all the additions again for the third time. All ok. Dealer said the new TSSM did not need to be married to the ECM on a Marelli bike. So, apparently, that wasn't it either. Since the bike started and all the lights worked ok I doubted it was a bad new TSSM. Looked deeper.
According to a diagram on the face of the original TSM itself it has one ground leg with all the other used positions carrying the various light signals. The wiring diagram in the Clymer manual shows it the same way. In the connector originally plugged on the TSM the ground leg was in an ostensibly unused position. Moved it to where it was shown to be according the TSM's marking and the Clymer wiring diagram. After that it all worked fine.
Apparently the otherwise unused pin location on the TSM is just another ground location within the module? Just guessing because it worked that way for the better part of nine years. And there's only the one ground leg.
The new alarm harness, however, plugs in looking for that ground in the location shown in the wiring diagram. Somehow the difference allowed light functions to work but not alarm functions.
Important thing is it's working now. Seemingly without issue. Took an hour and a half to find it and change it. Still have to strap a couple of harness points back down tomorrow evening. But at least the troubling part is done.