One bolt will thread into the power block shaft, the other will not, that one is for the stock clutch.
Do you have a manual?
http://www.atlanticpaints.com/Manuals/PDF%20Files/PILOT%20FL400.pdf scroll to page 104 (pdf page) manual section 10-0
Then page 108 (10-4)...you'll need a way to hold the clutch (crank) from turning while you loosen the crank bolt. There are different ways to do this. My method was to remove the spark plug and feed a new, clean piece of cloth (won't fray) piece of rope into the cylinder. Feed enough in so that when you rotate the crank, the piston binds up on the rope. Put the the other piece (stepped shaft) into the clutch, into the crank, smaller diameter in first. The thread the bolt into the clutch shaft. Tighten it up until the clutch POPS off.
Use the tech link, top right corner, and look for the power bloc install steps by redrider.
You can make a tool to hold the power bloc from rotating...or..I used a pipe wrench to grab one of the 3 slider housings. slid a piece of pipe over the wrench so that it rested onthe frame.
Hope this helps. Gto more questions...post away.