Don't do random things. Work through the circuit logically. Pick one of the inputs that isn't working as it should, identify the section of the 339 that it connects to, measure at the input and output of that buffer and make sure it changes. If it doesn't change when it should - there is your problem.
This does get more complicated as some chips are interconnected and this becomes more complex to fault find with a simple meter.
Be careful changing chips as these tracks are VERY fragile and you can cause more trouble than you already have by fiddling around here.
Perhaps it's time to send the board out to someone for a professional repair?