If both trucks are now registered by the engine numbers it will make it easier but you still should jump through the flaming hoops to make sure that you have everything squared away with the dmv.

Step one would be to go talk to your states dmv and if they have a vehicle inspection station run by the state it would be better to talk to the inspectors first to see what they want from you.
Here locally the inspections are done by people who either are or work for the state patrol and that is the best place to get a straight answer.

If you have titles to both vehicles it shouldn't be a problem except for the paperwork.

48 Chevy 3100 going back together with a 292 six and AX15 five speed.