the AutoDetect TCM is your best bet, or you can get a throttle box from CAC (or i believe jason at transmissiontuner dot com)..
the box I originally got from CAC (and still have in a drawer).. took the voltage reading from my drive-by-wire pedal and converts it to J1939..
that was what I used before I enabled and connected my J1939 link, it didnt affect my normal drive-by-wire operation.
the other method you could go is to forge your own mechanical cable-pull and use a mechanical-to-J1939 throttle box. sold by CAC and Jason also I believe... these equate an amount of cable pulled from the box to a J1939 throttle reading...
I havent used a J1708 to J1939 converter although as long as it sends throttle data it would be an option.. I built one but cant remember what I was going to use it for..
supposedly the WTEC-II TCMs were built to use J1708 as the throttle input.. at least some of them.. many of them used an analog throttle (a TPS sensor that sent a return voltage based on position).. I have next to no experience with WTEC-II stuff so i havent tested..
this is one of CAC TPS units for mechanical use..
they also make an electronic version.. the one I have and had connected to my 444E prior..
the all analog throttle and auto-detect TCM are often CAT throttles.. as caterpillar was the first to install electronic transmissions on the electronic engines.. the 8.3 was a favorite to get the 3000 series and the 3116 / 3208 saw a few as well..
if you are going 6 speed 1000/2000, then I doubt you'll find many TCMs that are auto detect. most will be J1939..
again I have ended up forgin my own path to get to my beautifully shifting and responding set up.. everything from engine mods to trans tuning, boards, etc..
when thinking about how this stuff works, cruise control is another issue altogether.. as the pedal stays at 0% when on cruise in a T444E.. which can create a host of issues from no downshifting to shifting in a non modulated state.. this is why I went J1939 and enhanced the data stream to feed the TCM as much cruise info as i could, if you dont use the cruise control then its probably a noin issue for you.