Regarding stereo wiring, I took the power feed from the fuse box in the engine bay (you can bolt it to one of the 2 nuts on the main large power cable in there). Then ran it into the rear boot via one of the gromets, then between the outside panel (guard) above the wheel arch and the engine bay metal work and into the cabin. It comes out on the side near the seatbelt mechanism/rear speakers sort of area.
Its a bit of PITA to get the cable through, but i inserted a coat hanger wire from the interior until it poked out into the boot, and pulled the wires thruogh. Pull and extra bit of wire/string at the same incase you need to run more wires later to make it easy.
I had an amp in the cavity under the lid behind the seat. You can earth the amp directly to chassis nearby as you said, just make sure its got a decent connection (ie sand a bit of paint off under the eyelet you are bolting. There are heaps of bolts you could use in that area for a connection point, and use just as beefy a cable as the power supply. And fit the fuse as close as possible to the power connection point.
To run the wiring between there and the deck, I ran it just inside the sills. If you pull the plastic sill converings off and unhook the carpet, you will see looms runnign there, i just added to them. Its easy to get to.
Its good practice to seperate your power leads from your line level signal (RCA) leads/speaker wires to minimise interference, but I have combined them previously in other cars and didnt have any issues with interference. I powered the deck from the fuse box near the accelarator pedal.
BTW, the exhaust manifold looks awesome, talk about mechanical p*rn!!
Cheers