SHOooo:
The remote(s) for the remote starter & alarm don't lock/unlock the doors? You might want to check with an installer to see if the system is capable and installed properly. It would seem frustrating to have to use one remote to lock/unlock the doors, one to arm/disarm the alarm, and yet another to start the car remotely (if I'm reading your post correctly). In this day and age, you should be able to do it all with one remote.
If you do need factory remotes, do a seller search on eBay for 'marks-auto'. This guy sells them in pairs (although that's not exactly clear in his auctions) for a starting bid of $21.99, or Buy-it-Now price of $29.99. I just got a couple from him today, they're brand new with batteries and work perfectly. PLUS, he includes the programming instructions and ships really fast. He lists the same remotes under various vehicles (the auction I used was listed for Mustangs), but the key is as long as the FCC ID is GQ43VT4T *AND* it has 4 buttons (Lock, Unlock, Panic & Trunk), that remote will work for you.
Good luck!
-Chris