1. Yes, the clock can start and stop. If you waive your right to a speedy trial, you can withdraw that waive. Withdrawal starts the clock over.....even if the first waiver came on the 44th day. Once the waiver is pulled, a new 45 day time period starts.
2. When you are asked if you waive time, that becoems a general waiver.
3. Unless you state you are specially waiving time to a specific day, that is a general time waiver that must be pulled to start the clock again.
Bottom line. There is a 45 day period unless you give a waiver or the court finds "good cause"--a finding that can be appealed. Giving dealines for the production of discovery and the court extending that period has NOTHING to do with the speedy trial and time waiver issues.