With the CTS disconnected the ECM thinks you're driving on the north pole

It will stay in the cold startup and deliver WAAAY too much fuel. With this problem the car can never run right.
You can troubleshoot the CTS, if you wire a 640Ohm resistor in the harness the ECM should stay in open loop.
The ALDL has a bunch og pinouts The 1st 2 on the upper row are ground & test, connect a jumper between the 2, then you'll go into field service mode. If you use certain resistors (as a jumper) you can switch the other modes. The scanner does the same.
0Ohm (a short) Field Service mode
3,9KOhm resistor -> backup mode = limp home mode.
rpm, throttle position & CTS are used for controlling fuel delivery
10KOhm -> special or ALDL mode, rpm is locked at 1000 rpm
infinite (open) normal driving mode.
As you can see the ECM detects a major component failure (CTS) yet it relies on it to adjust rpm (the limp mode) Idle will be very erratic and fuel delivery will be way too much, the engine is running severely rich.
You can check w/ the10Kohm resistor, if the idle stays nicely at 1000 rpm the CTS is your main problem.
Don't drive like this too much, the lockup in the tranny won't work!
Also, the excess fuel is washing the oil off the cylinder bores, causing more wear
Marck