Well here's the thing, my engine blew (standard transmission) and I found a replacement engine but it was in an automatic. Will I have any issues putting this engine into my standard transmission? The guy at the junk yard said all I would need is a pilot bushing and it would work perfect.

 

On the '05 the pilot bushing is in the flywheel as I recall. 06 or 07 the revised the flywheel design but I don't know if there was any change to with regard to the bushing. You can see it in this pic if you look closely.

 

The engine will fit just fine. There were some engines with very minor internal differences for auto vs. manual to reduce vibrations or something. I'm running a engine from an auto in my manual v6.
The pilot bearing may require the larger outer ring as well, or if you buy one, it may come with it.