Difficult to say. Good you have the oldstyle carbs. I had no idea they'd fit well into the intake manifold engineside. Or has that manifold also been changed? Two things to realise: your CB500K3 has the same frame and air intake setup as a CB5
50K3. The 649A carbs
as a rack, dimensionwise is the same as a rack of 627B carbs that was on the CB500, K1 and K2 elsewhere. Carbs were only jetted differently. The
racks are dimensioned the same. You do not need that cover (btw I would
not call it a restrictor) only when you continue the #78 main jets. The
old model CB500s (so not your K3) have the same frame as the CB550, CB550K1 and CB550K2. These models (not imported in EU) happen to have the same dimensioned oldstyle carb racks as were on the CB500, CB500K1 and CB500K2. So an owner of a CB550K3 that was tired of the PDcarbs and had them replaced by the oldstyle carb rack, could give you first hand advice. I hope he will chime in.

As far as
running I don't foresee so much difference in having the K3 filtercase set-up or the K2's. The engine itself is 100% identical to the CB500 models before yours, so it will run. The K3s with their #90 main jets were known lean. You have a 4-1, so I'd start with the #100 main jets and then have some trial and error with the position of the airscrews. I would leave the needles as they are.
My choice for the gaskets would be aftermarket (cheaper). So far I haven't read bad reports. The original CB500 filter element is available through Dave Silver
https://www.davidsilverspares.co.uk/CB500K2-FOUR-1973-USA/part_61806/. Silver also has a K3 aftermarket airfilter
https://www.davidsilverspares.co.uk/CB550K3/part_28991/ If the steel spring that fixates the filter element is not available, you can make one yourself. I have seen that steel used in packaging, to keep cargo together like on on pallets.
If you are going to use the K3 airbox and all, you will have to close the breather's entrance (which is a nuisance anyway, that breather I mean). Whatever setup you are going to use,
as far as tuning, I'd concentrate on the main jets. I can understand your dilemma as far as the rubber boots airfilter side. Sorry, I just don't know if K3 boots fit well into an oldstyle plenum and vice versa. Others may chime in.