first of all many thanks for that awesome work. you've done !
I am using an arduino Mega2560 R3 board and flashing just works fine with avrdude and the atmels switch application .. no need for USBasp ...
Currently I am only using the board to connect accelerometer ADXL335 and plunger poti, which works fine up to now ... more to come ...
I have build lwclone from this git repo https://github.com/cithraidt/lwcloneu2
I just wonder whether the sources are the latest version as the last commit in the repo is form 2014 and I have seen that you have distributed the last binary package here 2 years later.