I've got one of those many piece puzzles now, I bought a Kawasali Mule 1000 Utility vehicle from a dairy that decided not to have it repaired. It came with the parts and fasterners in the little PU box on the back. I use the factory manual lots and am waiting for a couple gaskets to finish the engine install and see if it runs before I do much more. To your question, no the long studs/buts (including the one w/the infamous plug/cap that leaks) that clamp the cylinder between the head and block go under that top cover. For storage and security there is no reason you can't put those 2parts together for now with the fasterners finger tight. I think it is important to only tighten the fasteners when you know you won't forget to go back and fo it later.  A factory manual will be a big help (or even a Clymers one) as will this forum as some of us ehave been there. The manual just breaks the process into sections rather than sequential like we would like to have it.  The manual is pretty good at bolts size and location, parts diagram may be even more help, when you say stripped, do you mean the threads themselves or the hex head of the bolt or philips head on the screws.  For replacement fasterners good hardware stores will have some, some you will have to cut off as they may be an in between length. Cover screws should all project from the cover about the same height from the clamping sureface, the longer ones usually go through the hollow alignment dowels. The head cover has some very special requirements, look in the tech section for the pattern for them. Note that some use copper gaskets as they have oil pressure under them, consider getting new ones of these for a leak proof repair.  I've completely redone a couple of Honda singles(70's, 100's, 125's 200's, and 230 down to just parts and fasteners) and it is amazing how much they all look alike inside and how the Savage is similiar, just bigger -lots bigger. Take care, Max

I am not sure what do You want to do, but if You realy are trying to put head and head cover and after that to install it like an assy on the rest of the engine , the answer is NO !
How do You think to install the cam chain ?
What is so much about going step by step ?
Install the cylinder. Install the head. Install the cam chain and slide the cam shaft. Find the TDC and time the cam shaft. Put "LockTite" on the cam shaft screws and torque them. Install the head cover, paying attention to the bolt lenght. Adjust the valves and install the small valve covers. Have fun all the time !