Hey 3-Nation,
Good to see more people building these karts, I'm also currently building one with a 2008 Yamaha R6R 600cc engine.
+2 to the suggestion of using 4130 CrMo, lots of reinforcing/ bracing and gussets.
I also suggest that you add a fourth bearing hanger/carrier, and get a solid axle or one with a 5mm+ wall.
If you do end up redoing your extensions even with CrMo steel you want to have 4mm+ thick walls.
In regards to the headers being hot you can wrap them with exhaust wrap and/or put a piece of sheet metal between the back of the seat and the headers.
Also please do some front brakes, you can use the 4 pot calipers off the bike the engine came out of or similar. Just make up some brackets for them, it's a bit cheaper than commercial kart brakes and I believe they have better stopping power anyway.
Last thing would be to check out
http://www.motokarts.com/ They have a forum packed full of other peoples 100+ hp builds, however the forum is quite dead these days there is still lots of useful info.
Best of luck and happy building,
Datsun.