It's not an issue of what he paid, it's more of what he has in it. In the episode he said he had $7000 in it which includes the purchase price, shipping, and his overhead on the trip to Michigan to pick.
Considering it doesn't run, it's a 70's amateur restoration, likely full of "Rick's" parts, lots of incorrect parts, it's been sitting for 20+ years, and it's just a 29' coupe, he's probably close to his break even point right around $7000.
You have to wonder... The guy died a year ago (2010), the car sat for 21 or 22 years (1990 +-), and it was restored in the 70's (let's say 1975). So the car was driven post restoration for 15 years. What happened to the car that is was parked? Babbitt gone? Toss a rod? Or something else? Often the cars that are parked for a long time are done so for a reason!
I certainly wouldn't pay $7000 for that car as it sits in the episode.