I would advise not using 5th and 6th while towing or pulling if you go with a M6.. For the things you mentioned above, I don't see a major issue. (6 1/2' bed I am assuming). They are great trany's don't get me wrong, but those 2 gears won't last a long time if pushed. There just isn't a ton of material on them.
You still have the solid axle in the front of your truck?
Are you thinking bone stock LS1?
It appears you have already checked out the hybrid section on LS1tech, but the 01-02 f-body (also known as the truck manifolds) would give you the most clearence and are the second best flowing stock manifold. If you can fit the C5 Z06 manifolds go with those unless you are planing on using and aftermarket long tube header.
With my 63, I put the motor back as far as I though possible with out cutting the firewall. There is no way a M6 would fit right unless bucket seats were installed as the shifter would be basically under the seat. There is a ton of room in my truck to move the motor forward if I wanted (probably 12" or so). An M6 would then work.
If you want, I need to pull the dummy motor back out and put my M6 on it to put back in to the Camaro, I'd be happy to slide it in the truck with the M6 real quick, take some pics to show you where it would sit currently.
