Energy llinks convert EU into MJ at a 10:9 ratio (90%). The electrical engine converts EU to MJ at a 6:2 ratio (33%).
If you can, use the energy link.
Also keep in mind, that the electrical engine belongs to Forestry, a mod that we will loose in the next update.
Solved the problem.
We had renamed [2]ComputerCraft to ComputerCraft because otherwise it does not run, but this of course caused the problem where ComputerCraft would be loaded before redpower. I fixed this by renaming redpower from [1]RedPower-#### to A1Redpower-###
I had considered doing something like this, however, if you simply take a condenser with a small emc array over it, you could just "make" the cobble for free.