No.1 piece of advice? Dump the MSS_65 DME and SMG3 control.
There are so many interactions between the DME, DSC, ABS, Idle actuators, SMG, CAS, EWS, PDC (just kidding...maybe) that coding/programming/hacking the DME is challenging enough (although some prior work exists here in the public domain), and modifying the SMG programming for those other modules would likely cost more labor than any aspect of the mechanical work.
The Pectel SQ6 will work nicely with the S85 and they have a standalone transmission controller that can communicate with the SQ6 for smoother operation.
I researched this quite a bit in the last year or so for a potential Ultima GTR build (see here for a build by AutoBionics
I've also emailed a bit with a gent in Germany from the Pistonheads forum who is working on a an S85 Ultima and one of his challenges is the SQ6 control of the idle and throttle actuators. He is likely using a custom microcontroller in between the SQ6 and the idle/throttle actuators to convert the SQ-6 single throttle output into the two-stage PT-CAN signal for the idle and throttle actuators (remember, the idle actuators open fully before the throttle actuators crack open the butterfly valves.
The SQ6 is also capable of running the S85's ionic current system.
Good luck in your build, please document and post everything here! (we're greedy like that)