The Gen3 is an incredibly compact V8 for it's capacity. I think an auto would be your only option with a Boss 5.4 'cause you aren't going to get 3 pedals in your foot box
Have a look in my gallery as there are a bunch of pics of the LS1 and you can see the mounts. I'm using the Corvette mounts and the brackets on the chassis couldn't be easier. I can give you allmost all the dimensions for chassis brackets to suit this set up as I drew them up for Doug Pearce a while back.
Cheers