oh yeah? How did you feel about the ride quality/tuning of the motor? I do run a stock airbox but i've always been under the impression that if you go to a 4 into 1 you will need to rejet
If you remove the baffles in the standard mac muffler to make it louder, you will need to rejet.
I ran a cheap four into two system (stock head pipes/ aftermarket mufflers for 10-15 years, no rejet, on the 74 Cb550.
As I said earlier, I reanimated a 75 CB550K that came with a Mac 4 into 1 with the baffles intact. It had pod filters and ran sickly with the stock settings in the carbs. I put on the stock air box with a Uni NU4055 air filter instead of the stock paper one. It ran like all the other 550s I have, good power, good throttle response at all settings, decent economy It got so windy at 95 that I backed off the throttle. I expect it would have gone faster if I persisted. It would cruise at 80 without complaint or issues, other than rider buffeting.
I'm thinking of lowering the bike some to help get more feet on the ground at stops. Would going to a 4 into 1 cause any clearance issues?
Not if you keep the bike straight up.

But, in turns, probably. The springs compress in turns, bringing all the bike bits closer to the ground. A 4 into 1 makes scraping in left turns more likely than in right turns. But, if I recall correctly, the foot peg scrapes before the Mac 4 into 1 did. I must warn you that the MAC 4 into1 is not a performance muffler system. And, that it didn't work with the stock center stand, so the stand had to be removed. This is a headache for routine maintenance like chain lubing. I added a pic of the bike below.
If you use the common rear lowering blocks, it changes the spring angle. Doing so places more stress on the rear swing arm bushings and wears them out faster. Then the bike wobbles down the highway as the rear wheel "hunts" side to side due to swing arm play.
I don't know if you can simply find shorter shocks, but if you do, make sure you get stiffer springs to reduce the "squat" during higher G loading turns.
Have you tried a lowered/narrowed seat to get your feet on the ground?
Cheers,