OB2 port failure and O/D switch failure

[WiscoRedkneck]

Ok, so pretty confused right now and hoping for clarification.  Btw it's a bit of a read...

What happened, lost control of o/d switch/ could not disengage but trans acted normal, where I am at we have had some flooding so on my way to work in the dark I missed some high water around a bend and went through it at speed no deeper than the axles not even ten miles up the road o/d hunting began got to work a few miles down the road and called the builder of the transmission, this trans has maybe 20k on it and is still under warranty.

        He told me to come straight there after work finished work heading over to him trans acted normal again.  My immediate thoughts were weather pack/sensor problem so we decided to plug in a scanner and see what she said.  Long short three different scanners later no communication with pcm yet power present and all fuses good.  So we started manual diagnostics and found a bad casing on the output shaft speed sensor so we replaced it just because.

Now at this point stumped as all get out dead obd2 port and no control over o/d we went up the road to another builder who deals more with allison and has a built Cummins pulling truck for his opinion.  Talked over a bunch of ideas and decided to try his snap on scanner no comm he looked at me and said I think you have wiring problems to figure out.

 

So today I started working through started simple fuses first all good then I went on to thinking with 363,000 on the truck maybe I'm having pcm trouble so what's the easiest way for me to eliminate that possibility.  After consulting the book I found that with two small blade screw drivers you can pull the O/D button and test the O/D on off feature with a jumper wire this way testing wiring and overdrive sense in pcm, based on wiring diagram from book, everything works as it should.  Now to the OBD2 port I will state at this point I already know the pin out and have tested the port to find ccd+ bus signal prong dead. Throw my meter on again to get a baseline and see if anything changed and some how it did, ccd+ bus came back either by coincidence or somehow the bad O/D switch caused that pin to not have signal.

Question is do I still have other problems yet it just seams weird a switch would kill the OBD2 port.