I now run both pieces through the router seperately using my template first then Glue as Xanthus says. My template extends past the end of the fingerboard as it is a set neck tenon. Routing the two together after gluing would leave a huge gap under the template at the heel end after the fingerboard ends. I dont want to play with shims to keep the template stable while I rout. Also if I screw up I only ruin one piece. Sloted but not radiused board, I add the inlay before I glue or glue then radius.
If you already have a fingerboard / neck template here is how you make it so you can use pins. Now the pins can be anything solid. I would try a small rod of brass or aluminum 1/8" would be a good start as you can nip off a piece easy and its not flimsy. Even some 12 gage copper wire will work.
First I make some drill guides. A steel round with the size of the pin drilled through the middle. It does not matter if the hole is off center just straight through the insert (straight being the optimal word). I use a 1/2" MDF template so my insert is 1/2" long.
Put the inserts in the template in opposite corners, figure to stay away from the edge and any fret slots when you place them. One side is designated as the fingerboard on your template and one side as the neck (does not matter which). When you flip the template over it aligns the pins to the opposite piece. I usually drill the holes for the pins when the template is set up to rout, the fingerboard taper and the neck. Just remember to flip the template so the pins are not on opposite sides.
This one happens to be 1/16" pin (I had a left over box of them) and I wish it was bigger. Martin uses a short 1/4" roll pin, its huge.
The whole process takes only a few minutes to make and is well worth it if you use templates and hate chasing your fingerboard around when you glue.
Also Lee valley sells drill guides about $10 to convert your template using a pre drilled guide (removable) and insert. Just drill a hole and hammer in the insert, several minutes of work.
http://www.leevalley.com/wood/page.aspx?c=...180,42311,42321