Aaaaarrrrrgh!!!

the alpha, v1.8l, is available here . it's not the next release, which i'm still noodling with.

and yes, being able to distinguish between left and right alt is on the list

for whatever reasons I am reluctant to use any modifier keys with keyclone, I would suggest setting everything up without the use of shift alt or ctrl. Macaroon will let you easy bind keys to macros which should take up the slack, and you can set up macros so that if your mouse is over the target it does things different then if its not, although macaroon no longer seems supported ...