I more than a dozen App Engine apps (using cloud datastore and standard (not flex) GAE), and in my experience, the only non-negligible costs are:
1. Instances
2. Datastore reads
Instances tracks your request rate. For example, I have a very traditional web/db python app, and it usually has about 1 F1 instance per 0.1 requests/sec. (So if the request rate reached 0.5rps, then I'd have 5 instances.) This app has several hundred daily users, and it almost never needs more than one instance. (The first instance is free.) The only time my request rate goes up is when a bot ignores the crawl-delay in my robots.txt, or when somebody's calendar widget goes bonkers and starts hammering my ICS handler. I have alerts set up against budget, so when this happens I can investigate and block them with a firewall rule.
As for datastore reads, that's ridiculously hard to predict. It depends so much on what your app does, and how aggressively you cache frequently-accessed stuff. But looking at all my apps together, instances are usually half the bill, and datastore reads is the other half. So here's a quick estimator for monthly cost, based on my experience.
$ = 2 * ( ( floor(10 * RPS) - 1 ) * $36 )
RPS is requests per second, and you are probably over-estimating that by an order of magnitude.
-Joshua