Larry, I cam across a similar issue a number of years ago. The CHI 3V heads and intakes are dimensionally different than Ford 335 series heads. Besides the port location, the head is 1/4" wider in the direction the moves the face of the intake ports inward. This means CHI 3V Heads wont interchange with Ford dimensioned intakes and CHI 3V intakes wont mount to Ford spec 335 series heads without slotting the intake bolt holes.
I used this to advantage on fitting a dual plane 3V 9.5 intake to match C302B high port heads as the mismatch cause the ports and bolt holes to line up near perfectly on that combination but I actually had to mill a little off the intake land that seals the valley rail for it to land properly. When I inquired of CHI about the mismatch and suggested it may be appropriate to state such variances on their website they were nothing short of indignant with me as to why anyone would use anything but CHI lids with CHI heads.....which didn't sit too well with me but Ce La Vie. More recently I've noticed many of there intakes have slotted mounting holes but I don't know if enough to accommodate the 3V mismatch.
During that same CHI exchange, I asked if that was the case with the rest of their product line, namely the so-called "4V heads". They said 4Vs had standard 335 series port position and mounting pattern on both intake and exhaust. Just because they say that may not mean the head dimension you are observing isn't different and they have compensated on the other machining of the mounting locations. Just wondering if you've verified the exhaust side and port position are what you expected.
I did a write up on the subject over at the 351 forum; search "CHI 3V Heads and Intake" there. I'd say just make an aluminum spacer and screw/glue it to your block instead of the intake so the issue doesn't repeat in the event of future intake swaps.