Yes, it's in milliseconds. Increasing it makes sense and is worth a shot. You may also want to re-write the code to be more resilient/intelligent (more than 1 retry, increasing wait times for subsequent retries, etc). I stumbled onto this javascript implementation of exponential backoff here:
Probably the easiest thing to do though is to limit the number of calls you make. If you have multiple scripts checking urls, you will reach your daily and hourly quotas much quicker. I believe these quotas are per user, so if someone else (or a different login) schedules/executes them, you will be hitting different quotas. You can also try and adjust the script so that it only checks enabled keywords that belong to enabled campaigns/ad groups. Last thing you can try is to do a first pass that saves all of the urls you want to check, you can deduplicate the urls, and THEN check the urls. That way you don't end up checking the same url several times (it's possible you have several keywords/ads with the same destination url).
Cheers,
Alex