Why does restarting MongoDB 3.0.x boost performance?
I believe the slowdown is caused by running in Windows. I am going to attempt this on a Linux box once our new server arrives.

However, the 26GB limit is because of the WiredTiger default configuration which only caches 50% up to max ram.

You can change this using the http://docs.mongodb.org/v3.0/reference/configuration-options/#storage.wiredTiger.engineConfig.cacheSizeGB option.