2004 TRX 400ex – Top End

Recently purchased a 400ex off craigslist; When doing some basic maintenance, I found that the head cover was missing a few bolts. I ordered OEM replacements for the missing ones. When installing them, I found that the two on the left side (facing forward) would not mate correctly. I also found that the OEM version did not match the one that I pulled out. Also, after looking down into the other hole, is seems to be some sort of reduction. Neither of these seem correct to me. idk what was done before as I was told the engine was stock. With that being said, I was planning on just pulling the head cover off and assessing any potential damage now while I have the bike stripped. Question 1) Is this a simple task (I have a pdf service manual)? 2) Is there anything that you recommend doing while I have the cover off? Replace gasket, valve seals, etc?