I wouldn't worry about the bolts, put em back in, and snug them gently. clean them well, and use some blue loctite if you are worried about them.
as for the side plate, I'd just clean it and see if it seeps oil, or if it's spray from somewhere else. snugging up the bolts a tad shouldn't hurt though... (use a 1/4" ratchet ONLY!!!) they are thin bolts, so don't make them too tight.
as mentioned, you can safely remove the VCV, but it does no harm to leave it either.

oh, and I'd use a quarter car wash and soap, and spray that engine, and get it all grime free before too much more work is done.

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John HAUL AWAY, OR CRUSHED CARS!!! HELP ME keep the cars out of the crusher! A/C Thread
"as I ride with my a/c on... I have fond memories of sweaty oily saturdays and spewing R12 into the air. THANKS for all you do!

My drivers:
1987 190D 2.5Turbo
1987 560SL convertible
1987 190D 2.5-5SPEED!!!

1987 300TD
2005 Dodge Sprinter 2500 158"WB
1994GMC 2500 6.5Turbo truck... I had to put the ladder somewhere!