OK, so I have a question on the limits of the Speed Force Trait...

I am going to assume that the rule of three applies, BUT I just want to make sure. Lets say that I am using The Flash, and he is still on his starting dial with a 13 movement, and I have managed to get 6 speed force tokens on his card. I can only increase his speed by 3 for a total of 16 correct? I know there was the debate about the tokens and sidestep, but I have yet to see someone actually ask about this.

Yes the rule of three still applies to this. It is a modifier so it is capped at +3.

Just wanted to make sure before one of my players tries something funny, thanks.

Don't forget even once he hits the cap of +3 the tokens are still technically getting added. So even though +3 is the max the speed is technically still increasing so if his movement gets modified down the extra tokens can balance out whatever negatives he gets.

Excellent point. In other words, all modifiers are figured before the cap which happens at the time of use for final calculation. So 5 counters minus 1 perplex will still be +3 to speed but 5 counters minus 3 perplex would end up as +2 to speed.