Rob -
I remember doing the same thing in 1994. I drilled the holes EXACTLY where the manual told me to, and then discovered that the crossover weldment jammed up on the phenolic tabs when I moved the stick forward. (These are the tabs affixed to the aft face of the spar.) All you need to do is sand away the phenolic that's in the way and life is good. You should be able to contact the aft edge of the spar cap, although the control stop at the horizontal tail will keep this from happening.
If I accurately understand what you're saying, and you do what I did to fix it, then...
1) You have not compromised the structural integrity of the attachment of the control stick to the spar.
2) You can get full range of motion of the aileron tube through the cockpit closeout rib by relieving the hole as required. In fact, I recall attaching the aileron tube between the stick and the idler in the gear well and gradually enlarging the hole in the closeout rib until full range of motion was attained. In this scenario you have the same sized hole as intended, simply displaced about 1/16 inch (since it's halfway between the stick and the idler).
3) You should have no problems with binding between the rod end bearing and the idler. But if you do, add another washer between the bearing and the idler and use the next longer bolt.
4) You have not changed any of the moment arms and therefore the handling qualities will not have changed.
5) You won't notice that the stick is 1/8 inch lower.
Using a bolt through a phenolic block as a hinge pin is bogus anyway, in my humble opinion. My plan is to use it until it gets sloppy, and if it ever does, I'll drill it out to maybe 1/2 inch and press a bushing in there. It would be even better to press in a rolling element bearing (ball bearing or needle bearing). But I figure that if it's good enough for all those other Lancairs out there it's probably good enough for me...
Good luck. Feel free to contact me off list if you have any other questions.
- Rob Wolf
p.s. Check the retracted landing gear clearance to the closeout rib before you micro it in place. You will find many Lancairs that have a small glass-to-glass patch in the whel well side of the cockpit closeout rib to keep the tire from rubbing. Mine included. I will note that I attached a spacer to the tire when I glued the rib in place specifically to prevent this from happening, but it still did.