Ford Repair: Pulsating idle after replacing alternator, active green and ross, green and ross

Question
Hi, here is my problem. I recently had my alternator changed on my 99 Mystique V6 by Canadian Tire. The car was idling perfectly with the old alternator, by after replacing it, its idle is pulsating right after starting. After a few minutes running it is idling normal, until the next start. Canadian Tire claims the battery has shortened two cells, killed the alternator in the first place and needs to be replaced. I had my doubts and had the battery checked by the local batter doctor and was assured that it was ok. It charges, hold the charge and has lots of starting power. I realize you cannot diagnose the problem remotely but am hoping you could tell me if they are right or wrong with their diagnose? I would like to bring it back for a "second opinion", but would like to get a second opinion from an expert first.

FYI I have had wrong diagnoses from Canadian Tire before, e.g. a burnt valve in my Cavalier V6, when it really was a plugged injector after they installed a new gas pump.

Thanks
Dirk

Answer
Hey there sorry it took me a while to get to this i forgot to go into vacation mode here. anyways. First advice i can give you is STOP going to canadian tire. We see many problems with repairs they try to perform. Almost weekly we get one in on a tow truck cause they messed it up so bad and gave up, sent it to us when it is usualy such a simple problem. Same goes with active green and ross, It seems that they are all backyard mechanics that could not make it in the dealership world, But im just ranting now.Ha
If a battery had two shorted cells, First of all the car would not start. there are 6 cells in the battery each producing 2.1 volts, That makes the battery produce an actual value of 12. 6 volts, if you short 2 cells out you now only have 8.4 volts, that is not enough, So that is the first wrong diagnosis and someone trying to make a bonus with upselling a battery for no reason Although there are times when the battery fails and the altenator follows behind it, If a proper load test is done to the battery and checks out ok then you have nothing to worry about.
The altenator on theses v6 engine are fairly difficult to acess, so im asumming that the mechanic possibly did not put something back on the car properly like a vacuum line or something along those lines. that is only a possiblity, there is a chance that they put a cheap altenaor on the car as well. I hate to say this but there parts are sometimes as bad as there worksmenship. HORRIBLE> Take it to someone that knows a thing or two about cars and build  a relationship with that person, take your car only to that person everytime you need something and you will see much better results. unfortunatly in the car industry people are out to make money, so having someone that you can trust is always a good idea. Good luck, sorry for ranting but i hope it helps.
Chris P