Is there any way to gauge how many times connection times out over a length of time?

Yes, you can measure lag periods, but it might require a solid understanding of the network protocols you want to examine for lags. The easiest part is to capture the data, usually by going for a "capture to disk" kind of setup using the "Capture Options" dialog and saving the data to multiple trace files.

Then, you need to examine your captured trace files for lags by looking at the delta times between request and answer packets. First of all you need to set a column to "delta time displayed" mode, and then figure out where it shows higher values than it should. This is the hard part since there are network protocols where delays are sometimes higher without indicating a problem, while with others any delay means trouble.

Without knowledge about the protocol behavior you could try a statistical approach and gather data when everything is running fine and compare timings to problematic hours. If the delta time readings differ significantly your connection is in trouble - but keep in mind that it might still not be the ISP's fault. Maybe somebody in your location is using the line at the same time to download some large files, which will cause your real time communication to get delayed.

On the other hand - if your ISP is unstable you might want to look at this from a different angle. We had trouble with the line in our office a few years ago but we had a pretty decent router that could get us physical link statistics, like the "Signal to Noise Ratio" which is very important. In our case our 6MBit line had a SnR of about 6.5db, which was a catastrophic value. We ordered a different ISP line and downgraded the 6MBit line to 1MBit (because it had a static IP we still needed), and the SnR went up to 32db. Maybe your router/cable modem can give you statistics like that, too.