help re reprogramming fobs, alarm,etc!

The mechanic that worked on my V6 2000 cougar has screwed up my fobs as well as disengaged my addtional compatible security sytem for keyless enty: Omega Executive 4000, Model # AL-100-H. Now nothing works: regular keyless functions as well as my additional Omega alarm. He said the only way he could get the Omega alarm disarmed to work on it was to disconnect everything. (not true). The fobs worked fine when I took it to him as well as my additional alarm. Any suggestions of how to have him fix this screw up? (I won't be taking the car back to him after this..mechanic...yeah, right). I use the Cougar fobs for both systems. Any help would be most appreciated.
P.S. I hope the suggestion is not to take it to the Mercury dealer...I'm over him, too.