I am I getting OCD with flap Reflex
 

I have been doing some fine tuning with the rigging. I noticed that the flaps full up against the rear wing spar puts the flaps at -4 degrees (compared to the trailing upper skin of the wing). The flap edge is even with the bottom of the fuselage. But is not Reflex suppose to be -3. So should I leave it or set it to -3, which then the flap will not be resting against the spar.

I?d leave it.

To answer the OP?s original question...... yep.

Flush with the bottom skin of the fuse is where you want it. Leave it and rig your ailerons to match and your wingtips to match. Note that the elevator needs to be in trail when you rig the ailerons to match the flaps.

Make sure you don’t have a twist in your flaps. To do this, raise them all the way then measure the spacing of the flap spar rivets to the top wing skin trailing edge and compare inboard to outboard. The closer the better on this comparison, because the less twist you have in your flap, the better.

Soooo.. I rigged my ailerons to the rigging tool then set the flaps and wingtips to the ailerons. Did I do it wrong? The flaps are not flush with the fuse bottom skins. It is an RV 9

The process is different on a RV-10, which was the OP's question.

Thanks Bob, I wasn't aware they were different.

Got everything lined up as recommended. It all came together nice. Thanks all.