The reason the bolt came out with your finger is that tension is applied by the bolt head.
Bolts are held in place by their elasticity. When you spin it clockwise, the threads pull the bolt in, obviously. Once the head reaches the surface, the bolt will stretch as you turn it since the head is holding it back.
Sometimes a bolt will lose elasticity with time and use.
Get a torque wrench and check all of the applicable bolts are torqued to spec. That axle nut is usually 65 ft/lbs or more and the rear axle about the same. Very important.
Replace the swing arm bushings with brass. They're a slight interference fit, so you'll need to freeze the brass and heat the swingarm and press the two together, preferably without just beating it in.
I think I saw a ball in your clutch throw-out lever, is this correct? If so, keep track of this and make sure it's still round.
I also see that your clutch rod has a ball-end. You do not need this ball if you have this ball end. In my experience you won't be able to properly adjust the clutch if you have it and don't need it, or need it and don't have it. Did you ever kick the bike over to feel compression with the ball fitted?
As for wheels, I don't believe you'll comfortably fit more than a 1.85" rim on the front with a 3.00" tyre. 2.15" on the rear with a 90 or 100mm with 90% profile would be the max. I'd prefer a 90 back there. If the rubber is too wide, you lose sidewall structure.
I think CB350's have 18" front and rear, CL has 19" front. I believe a larger diameter improves stability, it'd be a good point to ask the aforementioned experts, as they have experience with motorcycle geometry.
Here's a tip; the rear rim on your bike is a 1.85"