Question. If my engine mount has down thrust (5 desgrees), the plane will have a tendancy to climb when throttle is applied right?

Kadet Senior ARF. I want to remove the down thrust for my Saito .91.

I could be wrong but I think the plane would fly level or pull down.
If when flying level at crusing speed and you throttle back and the plane climbs that would indicate to much down thrust.
Thats my opinion if you don't like it I have others .

I recommend to try to keep the down thrust as it is first. ARF manufacturer must have tested the airplane
and have concluded it needs such amount of down thrust to fly right.
Or your airpane wouldn't climb when you add power and you wish to reduce/remove the down thrust?
Then it looks like you can reduce or remove the down thrust.
As you say, there are other factors, wing incidence and C.G, which affect the flight characteristics.

Tsutomu Mabuchi

If the wing is flat bottomed, you need the down thrust to counter act the constant climbing that is prone to that type of airfoil.

Do not remove the down-thrust. Trust me. I did it with my trainer years ago and had a difficult time controlling it. The next day I put it back in. As mentioned by Deadeye, the flat-bottom airfoil has a natural tendency to climb. The lifting ability coupled with down-thrust is why trainers can fly so slow.
If you take out the down-thrust, you'll have to add a bunch of down elevator. Flight will not be easily predictable. You will not like it.
You could experiment with decreasing the wing's AOA... but then it really wouldn't be a trainer/easy-flyer anymore. You'd be better off moving up to an intermediate type airframe.

If you insist on trying it, cut two equal door-wedge shaped triangles and put them between the engine and mount to remove the down-thrust. Or, you could place a few washers behind the lower edge of the mount and the firewall.