I have an '03 sv1000 naked with M4 full system and a power commander 3usb. Does the power commander take care of timing retard or do I still need a TRE on top of this?
So...when you're saying 'TV's' you're meaning the PRIMARY (main controlled by the throttle cables) throttles...yes? If so...you've got a problem as there shouldn't be ANY play in the linkages. Both are spring loaded to go closed, and the adjustment screws where you synch them held by springs too....so they should be tight and when you move the front cylinder the rear should follow immediately with no play.
If you're meaning the STV's...then some play (like the 1/16" you mention) is in the linkages on both my TB's here, so that would be normal. The motor to primary STV plate has some slop, then the front to rear links have a bit more so it isn't exactly precise as the primary throttles. I set mine by closing the front plate then measuring the distance from top of TB to the inboard edge...then matched that on the rear. Thinking being they restrict the air most when closed, so that is where they should be closest to the same...whether they both make it exactly perpendicular to flow when fully open less a consideration.
Reset the STVSensor once you're happy with the adjustments...and it wouldn't hurt to check the main synch too along with the TPS just to make sure everyone is happy.That STVSensor allows you to play with them a little bit and you can adjust their 'sensitivity' if you will. With the sensor set to one end of the spec. the plates will be closed a bit more than if you set it to the other end of spec. Setting them to be more open (but still in spec) will 'free up' the power a little and might make the engine feel better....it did on mine at least. Then I drilled the plates which 'freed it up' even more, them went Full Monty with them all the way out.
It's all in how you want the throttle to deliver power....gently or aggressively.