I think your b-o-m is probably right on. That little narrow snout on the airbox and the accordion tube can't be good for power, and the filter is so close to the carbs that I don't think they can both draw from the whole air supply that's available.

Air cleaners should have zero impact on tuning. If you lost some low end with the box off, you may be able to tune it back in -- try going a wee tad richer on the carbs.

I've got K&Ns on my old cars because that's what fits physically. I don't think they flow better than good paper filters (not enough to matter, at least, and the whole thing about air molecules magically aligning is on a par with fuel line magnets), and they probably don't filter quite as well either.

Later HS6s used wide (2" or more) round paper filters that work really well... I wonder if there are some like that for HIFs???

Now let's see... the guy who happens to be selling Perluxes is the guy who says how much better it makes his car run. Hmmmmm... must be true, then.