I fully support restoring the air box components (along with a new air filter. I use the UNI NU-4055 foam/ reusable type). Used air box bits from the bone yard or bike "customizers" will probably be the best parts supply outlets. If Honda has them (probably), they will be expensive.
However, the breather system seems unlikely the cause of your engine run problems.
The assumption is always that the bike ran well off the show room floor.
So, if it is returned to that condition, it will run well enough to sell thousands of them. (History proved that!)
The resurection path should begin with the routine 3000 mile tune up check list. Most certainly, this should be done before "fine tuning" carbs.
Point gap, point timing, spark plugs - clean and properly gaped, tappets adjusted cold, and a compression check wouldn't hurt while "bringing back" a motorcycle.
If all the above are in a "known" state, then the carbs are addressed.
"Clean" means different things to different people.
So, "very rich", could mean that the mains emulsion tube wasn't removed and cleaned during the cleaning process.
Or,... that a main jet oring is corrupted, or that the main jet retention springs are missing, or that the slide needles are set too high, or that the slide needle jet is damaged.
...Or that the float valves are not stopping fuel flow, or that the floats are set incorrectly.
If you have it running, check the head pipe temps can lead you to a dead cylinder. Since the carbs use different fuel paths depending on throttle position, you can use this info combined with a cooler head pipe to refine where scrutiny is warranted.
For example, a cold head pipe at idle points to a carb with pilot circuit issues.
These are some ideas for you to investigate. The more solid data you can provide us, the more directed a response can be made toward a solution.
Cheers,