Hey Rex,
I agree with Thomas on this. As stated above, You should do it extremely slow over a period of months for both of your sumps. I would take out a handful or two every week, and as stated by Thomas, go with rocks about Tenis Ball sized. I wouldn't really base it all on size and pounds of the live rock. Different live rock has a different density. I would see how much your sump can support. Remember to do it very slowely!
One thing that no one meantioned, was that you should raise the water level in your sump. Having the water slowely trickle down the rock can be much worse than having the water trickle down the bio balls. Make sure your rock are completely submurged underwater.
I saw how difficult it was to have to raise the water level in your sump, I would work on it. I would try adding some RO water to the sump slowely, and watch what happens. I would see how far you could get the water level too. What return pump are you currently using to bring the water from the sump, back up to the tank? If this powerhead isn't bringing up enough water, the right sump might overflow. If it's bringing up too much water, that could be one reason why one sumps water level cannot really be raised as much as the other one. I don't think it's that the syphon is too small, although that could be one factor contributing to this. If you somehow cannot raise the water level in the sump without the sump with the skimmer overflowing, you might want to just go easy on the rock. Only pile as much as the waterline supports.
Graham