99 Saturn SL1

Those two year SL1 transmission have different part number's they will bolt even a SL2 transmission would bolt up. So the only code your getting is a Code p0706?Your not getting any gear ratio code's?Have you tried adjusting the selector switch?

So why did you end up changing the transmission?Here is the instructions on how to adjust the selector switch I also posted a diagram of where the leads from the ohms meter are hooked. Is this how you adjusted it?I also posted the trouble tree for your code P0706 I would start by following that and let me know where it leads you.

Place transaxle in D (Drive). Use ohmmeter or continuity tester to check for continuity across terminals on switch. Loosen the mounting bolts and rotate the park neutral position switch from the left front fender towards the engine until continuity is achieved.
Tighten switch to case bolts. After switch to case bolts have been tightened, check continuity.

The PCM determines which gear is selected by a combination of opens and grounds in circuits 771, 772, and 773 at the transaxle park/neutral position switch. Each combination indicates a specific selection on the manual shift quadrant (P R, N, D, 2, or 3). Circuit 776 is either open or grounded to produce an even number of grounded circuits (771 772, 773, and 776). Invalid data indicates that the sum of the grounded circuits 771, 772, 773, and 776, in one of the manual shift quadrants is equal to a odd number.

DTC PARAMETERS
DTC P0706 is set when the PCM has detected an invalid bit pattern for more than 3.5 seconds, twice per ignition cycle

The difference between DTC P0706 and DTC P0705 is that a possible bit pattern error due to misadjustment could set a DTC P0706.

TEST DESCRIPTION

This step verifies the conditions for DTC P0706 still exist.
If the shift cable or switch is misadjusted, a DTC P0706 may set while in certain gear shift positions.
DTC P0706 may set due to one or more circuits being shorted to ground. By disconnecting the switch, the PCM should read all circuits as high and the Scan tool should display "OPEN."
This step will isolate an open circuit. As each individual circuit is grounded, the PCM/TC should see the low signal and the tool should display "INVALID."
The PCM/TCM supplies a 12 volt signal to each transaxle park/neutral position switch circuit. This step tests for that voltage.
DTC P0706 may have been set due to one of the circuits being shorted to voltage. This step verifies if short to voltage exists.
REPAIR VERIFICATION
Monitor DTC menu "Code Status" for "Pass Since Code Clear" and "Pass This Ignition Cycle." When both have passed, repair is verified.

Criteria for pass:

No active DTC set
Two valid selector positions decoded (must move shifter to obtain pass)
DIAGNOSTIC AIDS
When the PCM detects a fault in the circuit (open, ground, short) the PCM will open the circuit internally to protect the circuit.

If no circuit problems can be detected, check shift cable and switch adjustment.

This DTC will cause the transaxle to start out in 2nd gear.

IMPORTANT: Refer to chart from PCM/TC Diagnostic Trouble Code P0705 - transaxle park/neutral position switch Undefined Data.

So did you have the code P0706 with old transmission?Also did you use the selector switch that came with used transmission?

It's not really making sense then your using the same selector switch the same computer you had before even if the transmission was wrong some how I don't see it setting that code. The only thing that makes sense to me is the selector switch got broken or you just don't have it adjusted like you think you do. Or the shifter cable is miss adjusted which you said you adjusted which I never would have done that just because I replaced the transmission.