Going via Baja is really much better if you have the extra time. I've gone both ways ... and last time went Baja coming down and going home.
There are two Ferries in La Paz, one to Mazatlan and the other to Topolobambo. The Topo one puts you within spitting distance of El Fuerte. Many go this way, and guys on GS's and Vstroms have done it, so a dual sport can make it no problem.
Or ... if you want to ride Mex 16 again, you can simply jump on Mex 15 for a few miles North up to Ciudad Obregon. Just out of town, at Esparanza, turn North East on 117 which leads you to Mex 12. Mex 12 intersects Mex 16 (where you found the Army check points). From there, you know the way ... but as suggested, next time take the dirt cut off over to Creel and save about an hour or so.
Glad to hear the DR was flawless. Good prep and good maintenance always pay off riding in Mexico. Nothing left to chance!