So the engine on my 8 went out last week and I've been looking around to get it fixed, Here in Denver the best price I've gotten for a rebuild is about $3,000 + what ever other parts it may need.

I found two engines for sale, the first one is a 2004 w/ 52K miles on it for $2200

the second one is a 2007 W/ 77K miles on it for $2000.

Now to my understanding the later engines had some modifications and bugs fixed, so my question is which would be a better engine to put in my car?

It's a 2004, with manual transmission.

 

Neither.. pay the extra and have the rebuild.

A rotary engine can last beyond 200k or less than 50k, there's no way to tell. Without getting a compression test on either engine you could never be sure which one is in good condition.
Even then a compression test couldn't even predict the remaining life of an engine.

 

I concur.

 

See how much the rebuild costs and what they are offering. Our engine is fairly different from a rx7 one, it has its perks and the builder must have specific rx8 experience to warrant a decent job.
Another option would be to buy a remanufactured engine from a good builder like Mazmart (forum vendor here) or the likes.
If you really can't and must buy a used one...get the one with the best compression but not for 2000$.

 

I got mine from Mazda reman and it was $1600 with military discount, but otherwise Mazda sells them for $2001.

 

What's up with that $1 extra, plus tax...lol

 

That's Mazda price $2001. I paid after taxes $1800, with my discount. Mazda price wOuld be like $2300 after taxes.