It's specifically mongos processes running hot, right?
One thing you can do is check when they are consuming a lot of CPU - is it continuous? Is CPU usage noticeable before the queries start? Is high CPU only during what you call "high load"? Is it constantly high then? Or periodic?
I'm not clear what you mean by "2 shards per replica set". How many shards are in your cluster? How many nodes does each shard have (I assume each shard is a replica set of X members - how many is X)?
One config server running 3 - do you mean all three mongod processes for config servers are on the same physical box? That's really a bad idea and it defeats the point of having three config servers...
Single document point queries are not really very intensive - is your cluster fully balanced or might there be splitting and balancing going on still?
Asya