This may seem elementary for the vintage enduro experts but for me - not so much.
In my rebuild process the chain and sprockets need to be replaced on my CT3. Problem is I cant get the side cover off to get at it!
Do I need to remove the 2 screws holding the clutch adjustment screw in to remove that cover? 

Also some of my case cover screws are converted to hex heads some are not. Where can I find the hex head versions as I come across ones in need of replacement?

There is one (possibly two) locating dowel and covers can often get stuck on this - lots of wiggling around of the cover will normally see it come free (assuming that all of the screws/bolts are removed). The two screws for the clutch adjustment cover don't need removing.

Some places online and fleabay offer complete allen bolt kits, or you can buy individual bolts from places like Boltbase (the length and diameter of screws and bolts are usually shown within part numbers).

"Some places online and fleabay offer complete allen bolt kits, or you can buy individual bolts from places like Boltbase (the length and diameter of screws and bolts are usually shown within part numbers). "

Shame on you Alan or Allen, can't believe you're suggesting adorning that lovely CT3 with allen bolts.
You've been spending too much time on the RD forum

I think there are 4 screws holding the ignition cover and another 2 holding the inner/sprocket cover.  6 total.  Make sure you have them all removed.

You don't remove the 2 screws on the clutch adjuster mechanism.

Yes follow MarkT instructions and then pull your clutch lever in and it will pop out done it numerous times. Good luck 

I actually but grommets and all of my metric fasteners at Lowe's (big box home improvement store). If I am  unsure of the thread size, I take one in and check against the sizing board there.Faster and less expensive and no wait.