You probably tried to adjust the FetcherTimeoutMs to a higher value but the log still appears, and it seems to be ignoring your config line, wherever you put it.
As far as I noticed, this is a bug. The trick seems to be that it will always log Fetch timed out blabla waiting for 50ms, even though you set it to higher. In other words, it does respect your configuration line, but with some links it sill indeed times out, and when it does it logs “…waiting for 50ms” – regardless that you set i to eg. 600ms.

So what you need to do here is set FetcherTimeoutMs to even higher value (if you’re confortable with that it seems to be ok to set it from 1500 to 2000 ms as the next time it will pull it from cache), or check why is the web server taiking that long to serve that resource.

One thning you can do to speed this all up, is to have Pagespeed talk directly to the filesystem instead via http(s):// by using ModPagespeedLoadFromFile check some deatils on it here.