I'd look for a change in the mounting of the frame guard - versus the kickstarter position. Is the sub-frame snug? Did the guard get tweaked a little - maybe a few whacks with a friendly rubber mallet will put things back into shape... The kickstarter (and the bike itself) have very little time on them. I should know - it used to be my bike!
Given that, is the kickstart mounting bolt tight? The first thing that would wear would be the contact surface between the aluminum kick arm and the kickstart knuckle. Given that you have access to a mill, etc. - Look here for wear and, if necessary, insert a steel plate so that it is steel to steel versus steel to aluminum at this contact point.
jeff