Should be able to mine microcoin with the github version now, although given that its N factor is still low, performance won't be very good (It will be cpu bound by keccak). I believe cbuchner has plans to eventually push keccak to the GPU, but until then you might be better off with a scrypt-jane patched cgminer, although I haven't seen any binaries floating around so you might be stuck compiling that yourself as well.

I've just managed to get a personal stratum pool up and running. After several hours of fiddling with node.js implementations that weren't really cutting it I finally just set up MPOS. So now I'm thinking about doing some stratum modifications to include scrypt-jane parameters in the job transmissions, which would require modifying cudaminer to change configs on the fly. It would be nice to have config file where I can specify something like "GTX 780: 13, T12x32, L2 : 14, T12x28, L5" Right now I'm having to write scripts to handle different coins, configs, pools, and gpus. Eventually I'd like to set up a scrypt-jane multipool.

Cbuchner why is your 780 doing so poorly? I thought you were getting 3.6 kHs before lookup gaps. It looks like several of us are getting 5+ on Yacoin now.