auto tranny problem

my friend has a 1990 integra rs he just bought. his alternator has already failed and has been replaced. today he wanted to use my tools to install a CAI. so he came over and we found out he needs to relocate the battery before we can install it. so we put the stock intake back on. then he took me for a ride and he said the car was acting funny. it wasnt accelerating right. at idle it seemed like it wanted to stall. i asked him to let me drive it and i tried it out. the first thing i did was switch through the gears. in park and neutral everything was fine. however, when i switched to reverse, drive or any manual gears, the car sounded like it wanted to stall. i put it in drive and stepped on the gas. it lugged like i was taking off from a stop in 2nd gear. and i think thats what it was. he basically has no 1st gear. i floored it and it was exactly like trying to smash in 5th gear at 35pmh. it lugged like crazy. at about 2500rpm it picked up and then it shifted into 3rd fine. my first thought was that the tranny needed a rebuild. but then i remembered trannys rely on a signal from the MAF sensor. well, we had just messed with the vacuum lines trying to install the CAI, so its possible something could have been connected wrong while putting the stock intake back on or something. however i remember connecting everything right. there was only three lines. does anyone have any other ideas what could be wrong? maybe the alternator which i kinda doubt. but he said that ever since the new one was installed, the car sounded funny at idle. kinda like a spark plug was missing. this 1st gear problem however, wasnt present until after we were done. thank for any info

I would first double check your vacuum lines to see if that fixes the car from wanting to stall at idle and then deal with the shifting issues... do the 90 tegs have a MAF? I thought they had a MAP, but I could be wrong.

however if I am wrong in thinking it has a MAP and does in fact have a MAF sensor you should go out and get a can of brake clean and clean off the element with the brake clean and then blow it dry with an air hose gently so as not to damage it, it's probably one of the best quick things you can do for a car with a MAF.

It has a MAP sensor.
Like stated above I would double check all the vacuum lines. Also if you need to relocate the battery, you have the wrong intake. Take that one back and get the one that is made for your car.
Also I would check all the wires that are connected to the tranny and any wire harness' that are around the area that you were working on. Makle sure that they are tight and corrosion free.