Transmission Swap [need Some Advice]

Listen to what the shop is telling you. There are pitfalls in the swap depending on your expectations. Are you EXPECTING a plug and play swap? If so, the 1st problem you will run into is a transmission from a modular motor (SOHC or DOHC) will NOT bolt up to a V6.

The next problem will be the speed sensors. The 96-98 uses a VSS sensor. The 99+ uses an OSS sensor. The sensor used needs to match the wiring harness AND PCM. The sensor's output are not compatible with each other.

An extended range SpeedCal can convert OSS to VSS.

My advice, if you have to pay someone to do the swap for you, consider selling the car and getting what you want in the first place. The car will be worth more before the swap (resale wise) than after. The $$ spent to pay someone to do the swap could go to buying the car that you really want.

Manual/Automatic swaps have the best chance of making $$ sense when the owner is doing the work themselves. That make the labor free.

If the automatic transmission is really going out, then repair it and then decide what to do with the car.

Get a manual transmission, wiring harness, and drive shaft from a 96-98 model year V6. Should bolt right up. Will also need the brake/clutch pedal assemblies.

If you can locate a manual transmission salvage car from a 96 model year, get the PCM. Having a manual transmission PCM will avoid having a constant check engine light as well as the cost to custom program the automatic PCM. For the 96-97 MY, the PATS can be re-programmed by the user. I have posted the procedure many times.

After you put the price list of all the parts together, I would love to see what it comes to. Labor?

Correct. The V6 and modular motors have a different bolt pattern. So unless you find a transmission with a removable bell housing, to me it doesn't make sense to do this in two phases.