not sure what kind of problem

ok i havent posted in a while here. but im having a problem with alot of crazy things happening at the same time. i have a 91 integra ls with a 96 ls motor. these problems have occured since right before my tranny replacement which has been done 2 times so im sure its not associated witht the tranny in general. it is an automatic. ok it all started with the alternator being changed. i noticed shortly after that while in D the car idled very roughly. like dropped to 400 rpm or so. always in drive at the time. so i went to advanced and they tested the alternator. the alternator checked out. both diodes were good. so i had no idea what could be wrong. so ive been driving it now for about 4 months without fixing it just living with it. its gotten worse. i have funny check engine light and it comes on sometimes and usually only during wet weather. the codes have been as of late the 12 (egr) code 5 (map) code 17 (vehicle speed) but usually go off and come back on after 2 miles ofdriving then they go off for days or weeks. its always the same codes and usually the egr. i was told by the local acura experts that egr shouldnt affect the idle and really shouldnt affect anything. so next is vehicle speed sensor... this comes on only sometimes and it idles rough all the time well cept in park or neutral. so next is map and ive heard this can affect idle but wouldnt it affect idle all the time? ok so all this time i still think its alternator but could power affect idle i mean it is auto so its electronically controlled. but the alternator checks out. i dont know i guess what im trying to ask is has anyone had this problem or heard this problem before.

overview
rough idles while in gear
have had codes but nothing to affect and nothing to stay on
car drives fine after idle
help?

Thanks,
Bigmack
if i forgot any info needed please ask im pretty mechanically inclined

to solve your problems, you need to deal with the CELs first.

egr

http://www.automotiveforums.com/vbulletin/showthread.php?t=473201&highlight=egr

concerning the map and vss, you need to check the voltage and sensors themselves. its getting late and i dont really feel like going through the procedures right now, but, do a search or pick up a helms or haynes. the specs are in there.