Reg/ rec combo ($30) - Good idea
New battery agm - Agree
tapered steering all-balls bearings ($30) - Probably not necessary and not much of an upgrade in the real world
Paint the bike a metallic black, and either mask off, or paint new OEM white accents - I wouldn't touch the paint other than with a polishing rag
Paint the frame a satin black or gloss black, using 2k always - see above
New ebay seat cover ($55) - Nice touch
New aftermarket all chrome headlight ($50) - I wouldn't bother
New 1 size larger tires all around, not decided on brand yet - not recommended on stock rims. Check the tire manufacturer's website
new brake pads - "shoes" are for drums, pads are for disks
polish all aluminum - always a nice touch
euro low rise chrome bars, drill holes for wiring to be routed internally ($30) - the CL was a "Street Scrambler" and should have high bars
new 530 chain, or 520 o-ring kit ($30) vs ($150) - are you sure it's 530 or is it 525?
New short cable set ($35) and speedo/ tach cables ($25)
Fork seals ($12) - Good idea
Uni air filters ($30) - not a good idea with those particular carbs. I run them on BS40 CV crabs that are much easier to jet correctly. Talk to PJ.
Carb rebuild kit, try to get OEM - Talk to PJ
Check the engine health (I have no idea of compression etc, only thing I know is that the kickstart will spin the motor nicley), maybe do a rebuild with new rings etc, and new cam chain tensioner. - I would check compression and valve clearances and chain tension and it that's all good, go for it. Once you split the cases, you run out of excuses for not stripping it completely and that's how we get project creep.