By making your own I was speaking of doing the paperwork. This requries doing an ATF form 1 to make and register a NFA weapon, this is filled out in duplicate the form is available for download from
http://www.titleii.com then you contact your local chief of police or sherrif, they sign the form if they see fit, then this goes into the ATF with the $200 fee, and two fingerprint cards, and the form 5330.20 citizenship certification. with photos attatched to the forms. The ATF processes the forms and returns one copy to you. you have to mark the receiver or barrel with your name city state just like any mauf.
Then once the form is approved you may make the firearm. By make I mean in the legal sense. You legally made the gun. You are the legal manuf.
The easiest way would be for you to tell Troy what you want and have him make it with a barrel extension added to bring to 16" then when your forms are approved you remove the extension leaving the short barrel.
Or you can send parts and a receiver to Troy, or you can send him a complete rifle and ask him to shorten, or you can do any amount of the work you can do yourself.
You will have to contact Troy to see what he would want you to do explain he has to work with a rifle you register because he is a dealer and you can not buy short rifle from him, but he can return a rifle provided by you to him for repair.