if you truly have a converter from a 44 RE and a 46 RE trans or vise versa... NO GO. the 44 series is based off the 904, the 46 based off the 727/ the splines are smaller diameter on the 44 than the 46.

 

It turned out that TC was obviously from some older model of 46RE/A518 as it was all OK except of that one offset bolt which I resolved by grinding the hole oval.. As for later shifting problem, it was the governor pressure sensor/solenoid, I changed them both and the problem gone. Thanks everyone!