The sikaflex idea has some merit. I suspect that if you measure the widths
of your cracks over the period of a year, you would notice some variation.
If you fill those crack with wood, you are likely to pop the inlaid wood
out as either the 2 x6 or the inlay expands.

If you are still intent on inlaying with wood, I suggest making a "fence."
This is nothing more than a straight piece of wood sized so that when it
is screwed into the adjacent floor joint, the router base can ride along
it and cut your groove. Since the screws are in the joints, they are
invisible.

The other part of the eqation is that you must use a solid carbide up
spiral bit such as this one:

http://www.amazon.com/exec/obidos/tg...69469?v=glance

(repaste the URL if it is broken)

Any other bit will wander and plug up with shavings. Event with this bit
it is best to take multiple passes.

You will have no option except hand chiseling the last 2" of each joint
near the wall.

I hope this helps