You could have a few different issues going on here.
When testing the SMC with the spin the wheel and push on the caliper is a difficult thing to explain to folks. I've seen some folks take both hands and push hard enough to almost take the bike of the center stand and think because the wheel stopped that it passed the test! The SMC should only move 1-2mm at most, and you should be able to take just 1 finger or your thumb and GENTLY push forward to stop the wheel. You could push hard enough on a failing unit to still cause the rear wheel to stop.
The needle bearings at the lower pivot point, as well as the countersunk head of the bolt could be dry and binding also.
You say the bore looks good? Are you sure? Due to the angle of the piston, the bore normally wears on the inside top of the unit, and will appear to be a dark line, where the plate scores it.
Yes, air can and may cause some clanking or play in the SMC, the bleed procedure in the service manual should be followed correctly and in the proper sequence. You should also check out Jfheath's article on how to properly bleed the system and what to look for.
However, If you took the unit apart, this may all be a moot point, since Honda and the service manuel instructs you not to remove the assembly since the distance is set at the factory, and you will have no way of knowing if you reassembled it back to the factory position. Did you replace the C-clip correctly with the sharp edge pointing up? I ask because another member had his grenade on him and come apart after he fiddled with it.
My guess is this: Your SMC is/was on its way out, and that is why the piston is/was sticking. However to error on the side of safety (since it is a brake system) I would replace the entire unit due to the disassembly, and then lubricate the needle bearings, replace all the crush washers, and have the entire system bled correctly just to be safe.
YMMV