Theres an option in keyclone (I'm assuming your using keyclone) that says something like 'mouse focus', if you uncheck that you wont get the pause when moving your mouse over to other windows but you will have to click to activate that window (eg. if you move your mouse over to your slave to open its bag you'll need to double click but you wont get the pause).

As with the ctrl+r thing, turn it on on an alt then move your mouse back to your main and click on something (eg. open a bag) then look at the alts fps without moving the mouse over to it.

Turning off the sounds on your alts can help with performance.

I'd suggest turning off vertical sync to lift the limits on your fps (unless you see lines appearing on the terrain when you run around).