Here is the deal, swapped in 6.5/4l80e from 95 3500 2wd into my 89 3500 2wd ext cab dually, when I say swapped I mean EVERYTHING, all wiring, pcm, inst. cluster, heater box complete with a/c evap and drier, swapped accelerator pedal assy, everything! I also removed the elec ip and installed a mech DB2,
I have done all air intake upgrades listed in FAQ and 3 inch exghaust. I fabricated linkage from the acc pedal to operate throttle cable for the mech ip, I have a pot switch on boost sensor set at 19k resistance, I am making around 18 psi boost, I have pyro and trans temp gauges. trans temp runs around 180 to 200 (but its been cold here). 3.73 gears and 225/85/16. I removed a 6.2, 4.11, 4 spd combo.

The problem is this thing will break you neck (and trans mounts) when it shifts 1-2, and it will not shift until 3500 rpm unless you back off acc pedal a touch then it will shift anywhere from 2500 to 3500 2-3 shift is hard but not brutal and od and lockup work excellent.

From what I have gathered the trans is locked in full line pressure.
Everything worked perfect in donor vehicle before swap.
codes are always 17,18,29,34,36,43,48,62,85,99 I can clear them, drive it 20 miles and these are the codes, most because of the missing ip, but 48 and 99 seem to be the codes to chase but I do not know what to look for.

Thank you in advance for any help .

I would post this one in the 6.5 section. But it sounds ike you need a new chip and get a set-up that is compatible with your mechanical pump. Chances are that you don't have the accelorator pedal and the IP synched together correctly to give proper shifts. And the 4L80 from a 95 had the 1-2 accumulator seal problem that gave a delayed harsh shift from the 1-2 shift. A transgo kit will take care of the mechanical portion of your problem though.