Radiant barrier in the attic is an excellent idea. At the typical roof temperatures you see in the summer, even in a temperate climate, radiant transport of heat is significant and a properly installed radiant barrier can be very effective in blocking or reducing radiant transport of heat.
California Title 24 now requires some kind of radiant barrier. My house was built just before this requirement took effect but I elected to pay the small premium to use TechShield radiant barrier anyway and it has been worth it. I reviewed the AtticFoil site and they seem to have a good product for retrofit applications. Your plan sounds like a good idea and I don't see any major issues aside from the usual ones of "work carefully, try to avoid falling through your ceiling, prepare for the high temperatures up there, watch out for dust etc".
Do try to stay away from the "over-insulation" method as that loses effectiveness as dust builds up on the top (working side) of the barrier. Your plan to use the "open-ridge" method is the best as dust buildup on the bottom (working side) of the barrier is not as much of a problem.
Insulation of the ducts is not a binary yes/no question any more than attic insulation is. funkadelic understands this and that is why he plans to increase his attic insulation from R19 to R50.
Yet duct insulation is typically no more than R4 to R8 while carrying the coldest air in the house. It is the part of the HVAC system that has the least insulation while needing it the most.
No doubt there are some installers who think that as long as "cold" air comes out the register there is no problem but this ignores the question of how cold is the air at the end of the duct vs the air that went into the duct and how much cooling power has been lost in the duct.
Who would accept a water pipe that leaked half of the water it carried?
The Federal government has done many studies of ways to reduce duct loss because it does make a difference in your energy efficiency. There are even suggestions to move the HVAC ducts into conditioned space as this would cut duct heat/cooling losses to zero. I did this in my house.
For retrofit, moving ducts is impractical so the next best is to bury the ducts. You have an excellent opportunity to do this when you upgrade to R-50 of cellulose.
http://apps1.eere.energy.gov/buildings/publications/pdfs/building_america/ns/eemtg082011_a8_duct_retrofit.pdf
It sounds like you have a convective loop, in which case the reason why the fiberglass insulation was not as effective as you would have liked is because fiberglass is air-permeable. Since you have access to the duct itself, try sealing it off with a section of fitted and caulked insulation foam board or something. Doesn't matter where in the duct you do it; the important part is to stop the movement of air to break the loop.
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You need to make sure they can get enough makeup air for combustion, so that they don't backdraft, but yes, you can and should cover the top, that is absolutely awful for any sort of energy efficiency.