There is no need to allow for the weight of the engine and test mount in your set-up when you measure thrust, the engine is not trying to lift it... assuming you are testing with engine crankshaft horizontal. Just be sure your set up is as friction free and level as possible. I wouldn't bother trying to allow for the little friction that you have in the system as the vibration will reduce it's affect to negligible anyhow.

I think your basic idea of using a skate board is a good one, and you'll have a lot of fun comparing props, mufflers, etc., and getting familiar with your engine without having to bother mounting it in an airplane.

Be sure to add safety travel limits in all directions so that there is no way your test stand could go on an unscheduled flight!