So long story short, my 07 Type S 6MT transmission is having issues and it's not possible to find another Type S transmission locally but 04-06 Base 6MT transmissions are available. So my question is are they a direct swap? Or are they different transmissions?

 

IIRC 04-06 has a different bell housing than the 07-08; so it wont fit.

What type of issues are you having?

 

Are you running synchromesh in it? If not, depending on the issues you're having, that could fix the problem.