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Ilker..

there could be a bunch of reasons why it would shift into third at such a high speed..

replacement 4L65E harnesses are available thru most transmission parts suppliers..

. there are several differences between years..

GM dealers can also supply them thru the parts department.

 you should be able to find something from this manufacturer..

http://www.rostrapowertrain.com/types/wire-harnesses/?makes=gm&transmissiontypes=4l60e-4-spd-rwd-1993-2012

you did not post an exact year so i can't tell you which circuits to OHM by disconnecting the PCM to verify the electronics..

 with many scan tools that display live data you can also check for codes.. look at the VSS signal..Vehicle speed sensor.. sometimes the solenoid operation.

you could also have debris in the valve body..

a clogged screen perhaps..  a hanging check ball or worn valve body separator plate.

improper torque used on the valve body.. can distort it and cause pistons to hang up..

because you had water in your transmission you could have rusted springs in the valve body or front pump..

EDIT  i screwed up.. i posted links to a 4L65E..

you have a 4T65E..  

this may help some

https://www.sonnax.com/tech_resources/566-gm-4t65-e-valve-body-layout

 just a wild guess...

those are CLICKABLE links.

4, 12, 13 and 14 are what i would look at first.. see if the instructions on each one of those covers your issue..