Here is the final update.
Out of 20 tkts requirement, I was able to book 14 confirmed tkts for this train 16381 - KANYAKUMARI EXP. out of 14, 8 are from Pune to Tirupati and 6 are from Mumbai to Tirupati, boarding at Pune from IRCTC site after struggling for almost 1 hour.
To know the station wise class wise quota, you need to login to IRCTC site after 12:30 AM on the 90th day (in advance). You cannot book the tkt but you can see the available tkts. Tkt booking starts at...
more...

8 AM on the 90th day (in advance).
When I checked the 3AC quota for Pune and Mumabi on 30-Oct-2011 for 28-Jan-2012 at 12:45 AM, there were 10 seats for 3AC for both Pune and Mumbai.
I guess this is shared quota as I was able to book only 14 confirmed tkts and rest 5 are wait listed tkts. Out of 5 WL tkts, 2 are booked from Pune; hence status is RLWL 1 and RLWL 2. Whereas 3 are booked from Mumbai (boarding at Pune) and the status is PQWL 1, PQWL 2 and PQWL 3. In total, I booked 14 confirmed 3AC tkts and 5 WL 3AC tkts.
Assuming no one else has booked any 3AC tkt other than me, it looks like there is only 14 tkts quota for Pune and Mumbai both combined for 3AC class.
Another interesting thing is I got 10 side lower and upper births ( 5 sets out of 9 sets of 72 births).
So strange....
I hope this information might be helpful for others.
Also, pls put some light on actual station wise quota for a particular class and why I got most of the side births.