My 02 clicks, but from somewhere else

recently, in first and sometimes second gear, when i go from neutral to first, there's a popping noise, metallic-sounding, and it also makes that sound if i'm coasting or low-revving, then punch the gas. Same if i do it in second. Sometimes, after alot of driving in hot weather, it'll even make the noise when i disengage from first to go to second. I suspect it's the master cylinder. Opinions? Any idea how expensive this is to fix? I've got 58k on the car, btw, but other than spirited driving maybe 10-20% of the time, i just have intake and exhaust, so who knows?