i kept hearing this whining noise from the passenger side windshield/dashboard>>>

Hmm. Only whining noise I've ever from inside a car were from the speakers. My 96 Accord used to emit a whining noise through the speakers that would be in sequence with the engine rpms until I bought a new stereo and 4 new speakers. Has something to do with a bad ground.

ok then a week later, my alternator went out>>>

Delphi alternators are garbage. Some people strike luck with them, but they are the exception. Delphi is also a large supplier for General Motors. In any case, Denso is far superior in quality and longevity, but apparently Denso doesn't carry alternators suitable for aything larger than a 4-cylinder.

Then it does this thing that after i start it up(warm or not) the RPM's get real low and the car shakes for just a few seconds and then they come back up and its fine.(?)>>>

Hmm. When was the last time you've had a tune-up? How many miles on the car? Might also be the the IAC (Idle control valve) ??...

Now i just went to go to the store and i push unlock and my car lights blink like its unlocking, but it doesn't unlock, and when you press lock, all doors lock but the driver door>>>

My power door locks have never worked properly on my 96 since I bought it, the back doors are completely inoperable. One of these days I'll get around to fixing them.

Oh and my back passenger window is slow>>>

Pretty common. My driver's window was slow and would even get stuck. It would eventually work, but it took forever. It went like that for two years until finally the regulator cable snapped. I salvaged a whole new regulator asembly from a 99, and so far it's been working..but it's still slow. I give it another 2 years...

oh and the 3rd brake light on the back dash board went out>>

Mine doesn't work either, and it isn't the bulbs. It worked for about an hour a couple mos. ago, then went out again. All initial connections seem fine, as do the fuses.

What next? Can any one give me some explanation? Please and thankyou.
98>>>

Well, it's a 6 year old car going on 7...sh!t is going to go out and break eventually. Join the club...