welcome to the SOHC4 forum.
... nice 550...
You'll get different opinions here which is nice
I like to ride my bikes often so...
imho....
I'd keep the airbox and side covers. It's way easier to make it run better.
It looks like you've got velocity stacks on there now and if you say it's running well then the PO must have tuned 'em. (But how will you know how well it might run with the airbox?)
And at least put on a fork brace.. but better... a fender. One puddle can splatter a lot of shht.
Now on the other hand ....if I didn't care to ride everywhere ...
I'd say go all out..
Clear out the side covers and what's behind 'em... looks cool when that's opened up.
Remove, cut off, or drill holes in whatever you can.
You can also remove every other spoke for a more open aired wheel look...
(j.k. ... that may be a bad idea... but it's probably been done)
Either way I think the key word is... enjoy