What kind of paint did you use? If it's acrylic you need to be careful fixing the Future because anything that will dissolve the Future may also dissolve the acrylic paint.
Windex will remove Future and usually (note that I said "Usually") won't bother acrylic paint if it is thoroughly cured. For the areas that ran some Windex on a Q-tip and GENTLE rubbing might be in order.
I don't thin Future at all, but as Transblu said, thin coats are important. It is already so thin that it can run pretty easily. Spray on a thin coat, let it sit for about 20 minutes, and spray on another thin coat. Repeat until you get the finish you like. I spray at about 10-15 psi from about 4" to 6" from the surface of the model.
Anthing used on the canopy to dull the frame is going to dull the clear parts as well. You can try mixing some Tamiya XF-21 Flat Base with Future (About 3 parts Future to 1 part XF-21) and then painting it over the frame with a very small brush, but it will give a dull coat to any of the clear parts that you get it on as well.