ZF6 Converted tuning

[arejay]

Having a few issues with choosing which tunes to use with a 2002 f-250. had a 4r100, blew too many of those up and decided to zf6 swap it. thats where all the issues started.
Since doing the swap, a few things have been noted. Cannot go into 4LO. no way to tell the pcm that the column is in neutral. Figured bypassing neutral safety would have fixed issue but didn't. Curious if a custom tune would be able to tell the pcm it is safe to shift to 4LO or give up and change to a manual transfer case lever.
Other big issue is a hesitation, or possible misfire/ jerk around 30-45% throttle. any gear range, any load percent, it will do it. Very annoying hauling a trailer.
Got hydra to get a bit more out of the truck. PCM says VDH4 on it, nothing is under the TNAA5S8 hex so went with TNAA4S2 hex for more tunes. still has misfire issue.
Went into TOAA5Z5 hex, which is for standard trans, and now the jerk is totally gone, however check engine light and check gauges lights are on dash and no trans temp gauge.
Curious if a custom tune would be able to mix both of those things together; a tune that runs off the standard platform and hex codes BUT is also able to read trans temp from a 4r100. I have no idea what the difference between what information would be read or why it would be an issue since the automatic pcm tunes can read the trans temp just fine, yet the standard pcm tunes can not. Any help or direction to start digging would be much appreciated