Welcome to BHQ.
I have no experience with the 2 into 1 pipe set up. But for trail riding, I prefer pro-circuits..they are by far my favorite low to mid pipe.
You really need to ask yourself how much your wanting to build it?
A timing plate is a good $40 spent. Get your head milled, or get a cool head with the right domes. If your not riding in water at all, I always run no air box on all my bikes. MAKE SURE you properly jet with any mods that change air or fuel flow...like pipes, filters, reeds, porting...etc.