To those who have been able to bring back trophies with them. Did you do anything to secure the horns in the duffel bag? It seems that they could be damaged very easily by just being loose in the bag and having piles of luggage placed on top of them. Any tips or suggestions?

While I haven't hunted in Tajik, I have brought horns back in my luggage from Azerbaijan and Kyrgyzstan. The horns are very tough but if you are concerned about damage just wrap them in some of your clothes. I use a hockey bag as my big duffle and I have a large pelican case for my camera gear that floats around inside it. I haven't experienced any problems with this method. Just put a lock on your zipper and ask for fragile tags/stickers...I'm not sure if airport folk pay them any attention but I have them in several languages all over my bags and I've yet to have anything damaged.

I believe the outfitter does help wrap and tape them up, but I will use that trick of filling in voids with clothing, etc... as well as the fragile stickers. thank you!

I've not had problems either. I take a large side opening river bag (dry bag that is waterproof). By all means bring the trophies back with you every time you can.
Make sure you have your CITIES in hand and give yourself plenty of time between flights (it could take a while to clear customs).
Good luck, but either way you're going to have a great adventure.