1999 YZ 125 boggy bottom-end

50:1 is a bit low oil for a 125, i would use more oil. it sounds like it is jetted to lean so you might want to find out what your jets are and take it from there. also, if the reeds and top end are worn this will also show in a loss of power and also the crispness you want

i'd try a moose reed spacer, and add two teeth to rear sprocket also for better bottom power.

your powervalve can be filled with carbon, or your powervalve timing can be off try a 32:1 mix of 93 octane gas and maxima super-m or castor-927

Since the bike is getting older, I'd start by pulling the carb and cleaning it real well first. While there, check the reeds for cracks. Also, as already mentioned, clean your power valve. This can be accomplished with oven cleaner, followed by soapy water (will need to pull the cylinder first). Just don't leave the oven cleaner on for more than a few minutes. Also, since your new to bikes, be aware that 125's require quite a bit of clutch use. You may just need to rev and clutch more. If all this fails, find someone who feels comfortable with jetting. The YZ125 is a great stock bike, and aftermarket parts don't help that much with most of us average riders, although I agree that adding a tooth or two to the rear sprocket can help a lot with gearing.