95 LeSabre MAJOR Electrical problem???

Have a 95 LeSabre, 3.8, "L" vin, dynoride trans, roughly 130k,bought used with 98k on it 4 yrs ago, previous owner took great care of it with ALL recipts as I do as well. No major issues up to about 6 months ago, headlights started flaring/surging while driving or at idle. Figured ALT and or a BATT./took it to auto zone/checked it out/both failed so I replaced both. No problem since up until about 3 weeks ago. Lights (headlights as well as interior)started flaring/surging, then rough idle at intermittent times, check engine light would come on and go off some times just real quick, pulling away from a stop the car would act as if I was hit very hard from behind(change in ash tray would be jolted out), other times the transmission would act as thought the clutch pack was allowing the fluid to by-pass it(would not engage while trying to pull away-act as though in Neutral) ,some times while pulling away from a stop it will "buck" unless I throttle very easily, then it only acts as if its missing a bit. Initially it started off as just the lights flaring again but as the past 3 weeks have expired all of the above problems come and go, but at least one of them happens every time I drive it now. The check engine light now also flashes, stays on for the length of the trip. I can shut the car off, pull the key out, start it up again and the problems will have switched to one or some of the others listed. I unfortunately had to take it to the dealer(the car has the OBDI with the OBDII connection) because I could not find anyone else with the right scanner. 125 for the diagnoses..Neutral Safety Switch..replaced it myself(650 for the repair at the dealer!!) ...still have the same problems.
Does anyone have any experience with this kind of problem? I am thinking the computer is faulty but really just guessing at this point.

It is possible that you may have PCM (computer problems) but that would not cause all the problems you described. When the transmission does not engage, is this soon after you start the engine when it is cold, or after it has been sitting overnight? Will it engage if you shift into 1st gear? Are you absolutely sure the battery cables are clean & tight? Have you ever changed the crank position sensor? Have you checked the battery positive cable to the main fuse/relay panel mounted on the firewall to see if the terminal is clean & tight.

Word of caution, always remove the negative (-) battery cable first when working on anything electrical. Electrical surges & spikes can damage computers, but check the obvious things first!

I have checked all the battery terminal ends-all are clean and look like good connection. Replaced ALL the vacuum lines and could not find a fuse that needed to be replaced but did check. The trans problems are just as intermittent as the other problems. It seems to happen more once the car is warmed up BUT it has happened pulling away first thing in the morning too.I haven't tried to shift it down to 1st when this happens, it just does this then in a few seconds it engages.And no I've never replaced the crank positioning sensor.I could not find any recipts from the previous owner for any sensors being replaced either. Would that make all these problems happen?

OK well...had to take it to an Auto Electric shop this morning. I could only get it to engage the transmission in 1st or 2nd. After 3 hours of diagnostics they came to the conclusion the fairly new alternator was indicating to the puter it was putting out 25V!! That in turn was trying to shut down all the other systems because of the faulty operation. Somewhere among all of these intermittent problems the alternator and the puter gave out. So their best guess is the fairly new alternator killed the pc which MAY have damaged the transmission. Because its electronic, can't tell if the tranny is shot until the other two items are repaired. I have already sunk roughly 500 into this problem and now for the shop to repair the problem as it sits will cost me $1000! I am however considering replacing the both of them myself and in fact have already removed both of them. My concern is if I was to get one from a junkyard or buy one, do I have to swap the blue chip out inside the old one or is that what is shot? The shop mentioned a "reprogramming" cost on top of all the other work.Supposably to reprogram the new one to the old one. Is this necessary or just a nother way to make money for them? PLEASE, if someone has any knowledge of this proceedure I really need to know. The car is not worth more than 1200 and I can definitely NOT afford to have any more "shop" fees. I don't know if I should tuck my tail between and walk or go the 200 for another pc and try it myself.
:banghead:Between a rock and a hard spot

No programming required, just change the prom from the old one to the new. You should have a warranty on the alternator, no older than it is. Remove the red insulation over the positive battery cable and pull all the cables out. Look at the terminals & where the wires are crimped to the terminal, your looking for corrosion! Corrosion in this area has been the cause of many alternator & PCM failures!! Click Here (http://www.automotiveforums.com/vbulletin/showthread.php?t=966810&page=2) & read post # 30 & 31 for more info.

What an expensive and educational weekend and its only Saturday evening! I decided to at least swap out the warrentied alternator and pay the little bit of money at the local pick-and-pull for the pc. I had nothing to loss but another 40 or 50 bucks right? Glad I didn't give in. The PROM was in fact interchangable (thanks for the know how by the way) and after much back and forth with the parts place replacing the alternator(1st replacement bench tested bad,2nd one at a different store was drop tested in shipment-the pully was partially crushed and would not budge and the third one had to be over nighted from a mid-western states store-the store manager here was extremely helpful in my "simple alternator replacement") it worked just like it had never had a problem. Alternator frying the puter wasn't really that expensive it was not being able to diagnose the problem myself with the very special scanner and then paying out the nose for two places to do it. Luckily the second place knew how to test the entire car instead of just guessing like the dealership did.
Thank you for all the helpful suggestions and instruction.