The "mixture issue": for many years, i have 'tuned' my 750 to the altitude where I was with the octane in the tank. It works very well. As you go higher, you want LESS octane, as it burns faster than higher octanes. In the oversquare 500/550/400F/650F engine, this is the best way to match up without changing the jets. In the longer-stroke 750 and 350F, it is slightly less sensitive, but if I have premium in the tank and climb, for instance, Mt. Evans (14,260 ft), I may lose the #2 and #3 plugs if I don't keep the revs on tap more than normal. The center cylinders run slightly hotter than the outers, so they don't appreciate the richer mix.
The plug caps: yours should be 7500 ohms, if OEM. They should not be more than 8300 ohms, and on one coil not more than 500 ohms different between them, or one side will get weaker spark. Higher ohms makes for longer duration (and cleaner plugs), so a quick test of what you have might be to get some of the DR7EA or XR22ES-U plugs in addition to the plug caps you have now: these add 2000 ohms to the circuit(s) and stretch the spark dwell a bit. BUT...if your caps are weak, with the contacts burning inside where they contact the resistor, the resistor plugs may make the spark jump to the block instead. With new 5000 ohm caps, this won't happen.
HP loss of these carb'd engines is about -1% of total output per 1000 feet altitude, all else being equal. So, by 8000 feet, the 500 is typically running about 32-ish HP at 7000 RPM. Higher-compression pistons (if they are NOT forged pistons) will reduce this effect by about 50%, as the efficiency stays higher. This is why the "Gentleman's Express" version of these bikes (590cc, made with 750 pistons) has been popular for many years. Way back when, Action Fours used to make some 1mm oversize 10.5:1 pistons for these bikes, and if the owner stayed with the stock cam this made for a mighty torquey 500, indeed! Then, the rear sprockets would lose a few teeth to make them smoother 80 MPH tourers, too. But, those who decided they wanted a "big cam" to go with the pistons discovered the efficiency was very low until 7000 RPM, so the bikes became a nuisance to ride. (Something to ponder...).
The 4-1 pipe will cause a very small "suction draw" in a minor RPM range where the only power "boost" will be felt. for the rest of the RPM range, it will not have any effect, simply because the collector pipe is WAY too short to extend the header-suction moment. In order to actually work, this pipe would have to be about 8" longer than the rear wheel...