Farooq,
Is your discharge time 30usec or your charging time ? Or worse still, both ?

1.) ideally you need a comparator to define the same precise voltage that you say "stop" at.

2.) It sounds you have much too little clock resolution - remember a 12 meg clock can only count at 1 meg rate or 1 usec/tick. With 1 in 50 uncertainty you can only ever have a 2% resoltion ! with 1 in 30 you will have 3% and I think thats where the problem is. As Charles said, though I don't think he quite meant it in this context sorting out your signal in the analogue domain saves a lot of trouble here in the digital !

3.) If you use a Dallas 80C320, you will have 4 times more clock to use, increasing your resolution 4 fold.

4.) If you can't, use the main 12 Meg clock to operate an external counter, stop it with yor end detector and read it from a PISO converter or something like that.It would only take three or four glue logic chips to do what you want.

Steve