LS2 from a GTO right? I just put an LS1 from an 05 GTO in an 82. Are you using the T56 also? If so, swap the hydraulic throwout for a camaro unit. The GTO uses a funky hard line out the bell with a small conenctor, it's next to impossible to get a connector for it. Tick makes an adapter but you need the original plastic ring that goes on it. Didn't have one. The F body TO is easy to get a hold of (new) and this makes isntalling the clutch line and a bleed line (otherwise hardly no access to bell are for bleeding) too.
On the engine, the GTO accy setup will work but you have to notch the dr. side engine mount for the alt. Mount plates need to be +1 offset to the rear, best choice would be multi pattern adjustable ones. Have pics if needed