Clipless pedals alone will make the LLD effects worse on the bike, because you won't be able to compensate by shifting your forefoot on the pedal.
You can get a drop-pedal for the long leg. You can put whatever kind of pedal body you want on it.
Shims work, too, for a relatively minor LLD.
If you've already compensated at the pelvis for your LLD, you might find a leather (or better yet, leather and sprung) saddle works better than a drop-pedal. After you've broken it in a little...
How much full-length lift is built into the outsole of your short-leg shoe? If riding on flat pedals with your modified shoe is working well for you, I'd suggest simply continuing with the flat pedals. (It's a whole lot cheaper!) There are many great grippy flat pedals out there. Several of us use BMX style pedals, even on racy looking road bikes.
If your LLD is minor enough that you can get away with just a heel lift inside the shoe, well, obviously that isn't going to do you any good on the bike. You need lift at the contact, which is the forefoot, not the heel.
ETA: this is a popular drop pedal:
http://www.hscycle.com/Pages/cantsandwedges.html