Try draining the gas out of the carb first cuz this ethenol gas suck then if that doesn't work clean the carb good, I use a toothbrush, carb cleaner, something small to clean out all the small passages and compresses air.
worked great on my plastics they were very dirty from sitting outside for a few years also scraped them with a razor blade to take most of the grime off then used steel wool to finish them off.
For the 88-06 all you have to do is unplug the box under the hood I for get which one it is right now and for the newer ones 03-06 http://www.blasterforum.com/do-yourself-20/03-06-tors-removal-diy-41973/ as for the clutch problem it will still start no matter whats wrong with the clutch as long...
I think the raptor 350 are a direct replacement and bolt right up but I am sure someone who knows better will chime in or you could try searching the forum to see.
It would be such a small hole to drain the oil out of I don't think you would have to worry about catching a rock unless it is a really tall and narrow rock.
Make sure the wires going to coil are connected good if your going to start buying parts I would start with coil since they are cheapest and easiest to replace.
Clean the threads up and start it on and put some pressure on the a arm and it should be enough to get the bolt on you are talking about the ball joint right if not don't pay attention to what I said.