You mentioned that the head had been reworked as well... Along with the timing (both cam and ignition) if the head was cleaned, depending on how much carbon was cleaned out, you may have increased the displacement back to near factory, would would require more fuel to keep the correct a/f ratio.
Also, if the head were shaved true it could cause the cam timing to be slightly off, since the effective length of the belt/chain will be slightly increased.
'97 Acura CL 2.2L 5spd
'03 Honda CR-V 2.4L EX 4wd Auto