dude, it does go... those guys obviously dunno shit coz have you ever placed the car in drive with no throttle and felt it eventually go from 1st to 2nd and then 3rd without yer foot on the gas!! It will shift into 1,2 and 3rd but will not slip into 4th or lock-up... when i did my conversion, i had the exact same problem.. Have a look in your engine bay.. you should have a 3pin connector sitting there with colours brown, orange and green (i think they r the colours) this is the connector for your auto TPS. Im assuming they didnt remove this harness when they put in the 4.0L. On the CFI, it sits towards the rear of the engine bay but on MPFI models it needs too reach the front. Cut the connector in the middle and add about 30-40cm of cable.. that should be enuf to reach the throttle body. On your 4.0L you will have 1 TPS.
Problem here is that the shaft on the throttle body wont allow you too simply add another TPS in tandum, so you will need to remove the throttle body (4 screws holding it to the intake manifold) and replace it with a throttle body that has the longer shaft (only came on the 4spd 3.9L MPFI). Im assuming here that the 3.9L and 4.0L have the same sized throttle body and are a direct exchange, can someone verify this?
Once you have it on and connected up you will have correct operation of yer auto again. BTW, the jolt you feel when its changing down is coz the auto is kicking down too early and will revert to normal operation when u get the TPS operational.