I'm reasonably sure the other PTMs are still clocked incorrectly. I haven't been able to work out where the "1CLK" and "2CLK" signals are coming from which clock the PTM on the Q133 or Master Card (I don't have the schematics in front of me, my TV is occupied at the moment).
They come from the RTC chip on the same board.
As shown above, the AIC (Audio Interface Card) interrupt test fails, as the AIC interrupt is entirely unhooked up at the moment. The AIC schematics in the service manual are partly hand-written and the scan quality is rather poor, so I haven't been able to work out very much about the AIC. To be fair, neither was Phil, based on the September 2009-vintage driver.
Phil apparently didn't know what that board was even called, judging by comments in the code. The Analogue Interface Card can be safely ignored; they were used to talk to analogue synths and were not only optional but scarce. The CMI-28 General Interface (SMIDI) and Q014 Four-Port ACIA were also optional. The Q077/Q087 HDD Controller was rarely used and unsupported; mostly they were replace by the Q007 card which merely completed the DMA chain.
It may interest you to know that the minimum board complement for operation - sans sound - is CMI-02, Q256, Q133, Q209, Q219 and QFC9. The CMI-02 and Q219 may also be removed to diagnose boot faults. With the above information you may be able to prioritize efforts. Knowing that half the mainframe cards are not only unimportant but completely optional should reduce stress somewhat.