There is a truck accessory drive that extends away from the front of the engine the most, and it's also somewhat taller than the other two. The next-shorter system is the serpentine drive assembly used on F-cars, such as the Camaro and Firebird. Finally, the Corvette system is the shortest. There is also a slight variation on the system used for the GTO engine that we believe is very close to, if not the same as, the F-car system in terms of depth. What you cannot do is interchange pulleys or brackets between these systems for obvious reasons. You also cannot use an F-car-style intake manifold with a truck accessory drive since the F-car system positions the throttle body below the level of the accessory drive, thus preventing the addition of an inlet air duct to the throttle body. You should also look over the placement of the A/C pump on these accessory drives since it could be troublesome when it comes to clearing the frame and/or front crossmember. This will take some careful measurements on your part to ensure the engine will clear your Pontiac's major suspension components. Engine placement is best served by using a Camaro/Firebird oil pan. The Corvette pan is very wide, while the truck pans are extremely deep.
As for the trans, the T56 six-speed that comes behind many LS1 engines is excellent, but as you noted, the shifter is located much farther back. McLeod now offers a shifter that can be positioned in one of two different mounts on the transmission; as a result it can be located almost anywhere along the length of the transmission, both fore and aft and side to side in a very wide arc.
There's also a warning: The T56 is a very large transmission, and depending upon the height of the engine in the chassis, the trans tunnel in the early A-bodies (Chevelle, Tempest/GTO, Cutlass/442, Skylark, etc.) is somewhat narrow. This may necessitate cutting the tunnel and raising it slightly to clear the transmission. This sounds worse than it really is, but some enthusiasts do not want to put the cutting torch to their cars. If this is a concern, you may want to consider something like the Tremec TKO-500 or TKO-600 five-speed overdrive transmission as an alternative. This is a much smaller transmission, and although it is a five-speed, the overdrive selection (either 0.82:1, 0.68:1, or 0.64:1) is similar to the Fifth-gear overdrive ratio in the T56, which varies from 0.70:1 through 0.80:1 and even 0.84:1, which is only 16 percent. The Viper overdrive is 0.74:1. Of course, Sixth gear is 0.50:1--or 50 percent--and used for highway cruising. Tremec sells these transmissions direct, but they are designed to be used with an old-style Chevy or Ford application. If the TKO-500 appeals to you, for example, you could use one of McLeod's modular bellhousings to adapt the LS1 engine to the trans. You would then have the choice to use either a mechanical or hydraulic clutch linkage for this swap. The hydraulic clutch linkage might be a better choice only because you will have to make some kind of adapter off the GEN III engine to mount the mechanical-clutch-linkage Z-bar pivot on the engine. Regardless of which transmission you choose, it sounds like a fun project. Let us know how it turns out.
McLeod Industries; Placentia, CA; 714/630-2764; mcleodind.com
Transmission Technologies (Tremec); Farmington Hills, MI; 800/401-9866; tremec.com