Whats wrong with my engine?

I have a 1992 Lumina 3.1L with 93K on it. The body of the car is in great shape so when the transmission went a few weeks ago I actually went ahead and swapped it out. I got the car back yesterday after the work was done and they did an oil change as well. Now my engine is knocking after it warms up and is pretty loud. Any ideas? The car sat for about a month between when the trans went and when it got fixed. I'm in Syracuse NY and its been frigid here for the last week or so too.