Engine Rumbling Affects Alternator...

[KAT0]

So I have an '89 240 coupe that recently received the DE swap from a '96. At first the car worked just fine, but after 80 miles, the car would no longer start (eventually we figured out it wasn't getting fuel). After replacing the fuel pump, I wanted to drive the car down the street to ensure it's drivable (changed a caliper due to broken bleeder valve). I barely made it out of the garage. As soon as I put the car into gear, the engine started to rumble real violently. I looked at my cluster to see if anything was the matter, and eventually all the lights turned on as they would when the alternator gives out. The weird thing is that the lights flicker on and off, thus leading me to believe the alternator has some loose connection. The only problem with that is that when I shift the car into neutral or park, it quiets down and nothing happens with the lights.

Because of that, I'm prepared to think that something is wrong with the tranny... Well, something with the transmission has gotten worse since the tranny was already starting to give.

Since this is the first car I've ever done anything other than the pure basics, I have no idea what to think.

Any help is greatly appreciated.