Transmission problem
 

I had a Dana 36 w/ 3:73 but pinion failed. Installed a Dana 44 w/ 3:54 and have tried to get my Hypertech program correct by changing tire size to offset gear ratio difference. Speed sensors seems to be in orbit. Vehicle speed seems slow and inaccurate. At 65 and above tranny downshifts into passing gear, will not shift into overdrive and stay under full thottle. Need advice on correcting situation.
Thanks,
MLM