possible tranny problem??

Ok, looking for a little help here guys. Well I just got a new fuel tank put in and had a power steering hose put in (god, what a nightmare that tank was..) and now this morning, my 88 marquis is running like...well, crap. Im kinda POd that the day after I pick the car up, its now acting bad but it seemed fine yesterday afternoon/night. I knew the first gear was a little funny some times and was a little rough if you drove it in for a while but now, the whole cars shakes pretty rough if it stays in first gear long enough. Its never been this bad and Im hopings its just because its getting colder our but it was still doing it after a 45 minute drive on the NJ parkway. Plus, after I parked I realized its making a rattling noise from underneath the car when I push the gas. Kinda sounds like its lightly backfiring, I dunno. Its bad enough I just sank 650 bucks in a car thats got a bluebook value of $450, but I really dont have the cash for a new tranny at all right now. I wouldnt be surprised if its the trans, its got 126,000 miles on a stock tranny. So any ideas here?

I would think rattling while in neutral it is in the motor. You very likely could have a timing chain going bad. A weak valve spring can cause backfiring.
Have the plugs and wires been replaced recently. I not sure when this car quit using a distributor. If you have a distributor I can tell you how to check the chain without pulling the timing cover.