Pleeeease help me!

First of all im new to the forums. My friend told me i should come here becasue of my problems...i have a 99 malibu ls with cat-back exhaust and an open air filter..anyway i was downtown (indianapolis) and i was getting ready to go home and i put the shifter past D and right into 3--when i did that i heard some really strange noise...like a eeeerrrr er er er, almost like a computer thinking really hard. well when i got home i put the shifter into 3, 2, and 1...it only made noise in 1 and 3. it made it worse in 1...it was constant unless i let off the brake and let the car coast then it evenutally stopped...less than 5mph. then again after i had been driving the car i got home and put it in 1st and the noise was a little louder...put it in 2nd, nothing- and put it in 3rd..made a little noise. Sorry this was long but ive never noticed this before--a 2 days ago someone unhooked my transmission wirign harness under the hood--near the radiator hose and hooked up a tranny modulator to adjust how it shifted..i only had that on there for maybe a mile then put it back on my buddies car..could that have thrown something off?----thanks for reading this.