I'd start with the suspension, that'll make the most difference in the real world.
There are little things you can do while the cases are apart though, Matching the barrel to the crankcase is pretty easy and should make it run a little harder. Also if you haven't already done so you should measure and set your squish. Also do your best to remove all the carbon from inside the expansion chamber, 100+ hours worth of carbon will kill the performance of that pipe.
If you do get an aftermarket complete crank, take it to your local engine builder and get him to check it's true. They might be able to improve on how it comes out of the box.