The Accumulator where you install the shift kit is easily accessible once you pull the transmission pan. The PCS is located once you remove the valve body cover. (access though pass side wheel area) Big job!
I would start by having your car scanned once you have driven a week after the last time you removed the battery terminals and post what codes are found.

The transmission cooler will not necessarily be a fix for it, but a cooler transmission is a happier transmission. If you do the shift kit like was mentioned, that may buy you more time before a dreaded rebuild is necessary.

I think I'm going to go with the shift kit. I really don't think I'm at risk for the trans going all that soon though. The car has literally only ever done that the two times it has set while running like in traffic. I have started having other problems with the car at this point. Intermittent none start. I'm afraid my BCM is going. Starter and ignition are under a year old. The fuel pump isn't kicking on but working fine after I disconnect and reconnect the battery. Every year since I have had it numerous thing fall apart as soon as it gets cold.

That sounds like no fun. I think having the car scanned is very important. Hopefully after the scan it will pinpoint other areas that may be troublesome.
The 2001 Malibu did have a recall for the fuel press regulator. You can go to the owners section on the GM site-recalls and type in your VIN# to see any outstanding recalls as well.
Sounds like a new fuel pump is required. IDK if any of the Gearheads have any ideas as to why you would have to disconnect the battery each time to get the fuel pump working. That is not good. Have you checked all the fuses?
As far as the shift kit is concerned I would want to see the P1811 code after scanning. Keep in mind that these computerized transmissions require a good state of engine tune /running well, to shift right too.

Did you ever remove the belt yet?

I haven't had a chance to do much at all. The car will not start AT ALL. When I to crank it I can hear the fuel pump switch on and the starter (that is new) clicks one time then nothing. I am not saying this of every dealership but the one here is owned and operated by a band of crooks. They own every dealership in the county so they use their monopoly to beat people while they are down. I am friends with a GM master tech but EVERYONE calls on him to fix their cars so its hard to persuade him to come out. He has the scan tool that is needed. I'm still working on that. as far as the transmission needing the car to be running good to operate properly I have meticulously maintained the car. You cant hear it running without popping the hood. It just seems to have an electric and cooling derailment every time i turn around. I spent a year tracking a wiring issue that was tripping the pass lock system last year. I wired the yellow signal wire to a toggle and tried the resistor trick and come to find out the though still attached the second wire on the starter cylinder was burnt and not completing the current. iv been told it sounds like the BCM. The engine in the car is top notch but all the extra crap surrounding it is junk. Im pulling my hair out with this car at this point. In 3 years I have poured 13k into this car. Gonna have to draw the line soon.

the resistor has to be wired to the bcm, and bypass the rest of the circuit, is that what you did?