I always thought "Mil power" was max power without afterburners. In the Tomcat, however, the "Mil power" mark on the throttle is well below this, at around halfway of the slider. I can give more power without lighting the burners. Also, the speed brake should close at mil power, which it doesn't do when the throttle passes the mark, only when I increase it to max power without afterburner. Is this correct? Or is just the mark on the throttle off?

The markings are referencing the "detents" the real throttles have that you probably don't have on your throttle, at least I don't on my TM Warthog outside of 'burner. In that case it comes down to mapping. Per NATOPS, you have to be in MIL >3 seconds to get the speedbrakes to retract. Reads like everything is fine in your set up if flying the B model. I use the mini-HUD to verify my throttle settings as well.