I ride about 75 to 100 hours of engine time a year, and have owned KX500s for at least 6 maybe 8 years out of 25 or so of riding. Have had windowed piston and stock. Different carbs and reeds, spacer, etc. Currently riding on a stock top end. What I have found out is that when it comes to this bike it is very tolerant of just about anything, and puts out good power with or without the window (and other mods) and with crappy or perfect jetting. Have had buddies with so much spooge coming out the back end it wasn't funny. Some setup the carb perfectly. We all climb the same hills, haul on the same sandwashes, and just generally have fun. Bikes can go 3, 4 hundred hours on top ends (with maintenance and good oil) and just don't care unless you go too lean.
Most important thing is to do the maintenance and if you are picky jet it perfect. If you want to put in a window fine, want to do the carb spacer or different reeds, fine. In the end all that may help some, but again the most important things you can do is the maintenance and JET the bike RIGHT.
One more thing, the KX500 is the most tolerant bike I have ever know when it comes to lean jetting. It won't complain much and will run a long time lean before it goes. Only lost one top end in hundreds of hour of engine time and it was my fault on the main. If you ride somewhere where you can ring the bike out in 5th for many seconds at a time (I do) go up one or two on the main. Only Danny Hamel could tell the difference in power and worse case you change the packing in your muffler more. If you never ring the bike out much (for many seconds at a time) you can live with the top end more lean.
From what I can tell Kawasaki pretty much got this engine right...hard to find anything that could run the 1000 so many times with (from what I know anyways) are somewhat stock motors? Bottom line Oscar if you ran it with the stock top end and went up on the main one or two sizes you could run that motor hard for years and probably never notice the difference with or without the mods...IMHO.