Wow.... Lots of stuff up in the air, here.
To the original post.... What engine do you have now?
A 3.5 or 3.9 will bolt up to the F40 6 speed used in the... 3.9 GTP(?)
The 3.6, which was not available with a manual, will require the F40 that is bolted to the 2.8 turbo, which came in the Saab 9-3.
Any 4 cylinder? I can't speak to those, but they do have a different bolt pattern than any of the V6 engines.
Me? I have a 2010 GT with a 3.5. May consider swapping to a 3.9, because they're essentially the same engine.
If I do that , I'll possibly (wet dream stuff, here) be doing an F23 trans or (more likely) a New Venture T550 from a 94 Cavalier.
The T550 is essentially the same trans as the Getrag 282 5 speed used since late '86, but the differential gears and some other stuff have been greatly strengthened.
It also has a hydraulic release bearing similar to the F40 and F23.
(FWIW... I have a T550 bolted to a 4.9 Caddy V8 in a Fiero, and it has held up nicely.)
The down-side of the F23? The gearing.
Any F23 available that will bolt to a 3.5 or 3.9 (which is the one that came from the 2.2 OHV Cavalier) will have 3.91 FDR gearing. Not ideal for a 3.5 or 3.9.
There is some mix-matching that can be done, that involves swapping bellhousing cases, and trans cases, but it's a complete pain in the ass. Do-able, but more trouble than most people here will want to deal with.
The F40? If it came from a G6 GTP/GXP, it will bolt straight to any GM pushrod 60 degree V6, including our 3.5 and 3.9s. If you can find a wrecked/donor car, you're golden. The downside is that replacement clutches are stupidly expensive. They also usually want you to replace the (dual mass) flywheel. Replacement flywheels are also available from the aftermarket, but again... stupidly expensive.
Sorry for the long, rambling post, but I've watched people do this sh!t with Fieros for years, and have a pretty good idea of what works and what doesn't.
(I also own a 2010 G6 GT, and am always looking for something interesting to do with it, so I'm here with ya'.
)
If you have any specific questions, shoot me a message. I will tell you what I know and what I don't. I have nothing to gain by BS'ing you. If I don't know, I'll tell you.