I have a couple of 600EX-RTs and a Canon 5DMkIII. I am using group mode (or manual mode) with the flashes set on manual. Why does the FEL not work in manual mode?! It works in ETTL. It seems like all of the functionality is there. Tell the flashes to fire at their settings (for example 1/4 power), and take a spot meter reading of the light power for the given ISO. Just like a flash meter would do. Why do the Canon engineers disable this ability?
The way Flash Exposure Lock works is that it locks the power level of flashes to what is metered to be a correct level during preflash. In manual mode, the power level of flashes is locked all the time anyway (to the level you have set it to) and there's no preflash to meter, so Flash Exposure Lock is just not relevant.
What you seem to be trying to achieve is to set aperture automatically according to the power level you have set on your flashes in manual mode. Setting your aperture is not part of what FEL does, so it wouldn't help you. It seems to work in E-TTL because first the camera meters ambient light to choose an aperture, then chooses flash power to match. Obviously, it can't do that second part with flashes in manual mode.
The solution here would be to switch to E-TTL, switch your camera into an exposure mode that automatically determines aperture (e.g. shutter priority) and adjust the ratio of flash groups to your liking. Regarding exposure, it shouldn't matter much at what exact power level the flashes fire as long as the ratio is what you want.