Tom, I also put the adjustment at the head stock.
I run the slot through the neck after the head stock angle has been cut. Depending on the type of truss rod you use, you may need to cut/drill a channel for the truss rod nut. I use a gibson style, single rod truss rod and need to cut the channel like this
This is the tool I had made to drill the channel
I drill the channel after the spline has been set in the neck but before the head stock veneer has been glued on.
You can still cut the truss rod slot and use it to align for your jigs.
I'm sure others will have some ideas, but I think we may need some more specifics to your query.
Rod True38685.6901388889
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