On spark plug wires: Here's another discussion about trying different wires for better MPG:
http://www.gassavers.org/showthread.php?t=8696
17 mpg is pretty good for that vehicle, I think.
Your holes have no effect on your fuel economy unless you run high RPM + wide open throttle a lot -- but if you did that you'd never get 17mpg from that vehicle. Your concern about more air to the MAF and therefore more fuel shouldn't be a worry for a these reasons:
- At low RPM and/or low throttle, the airbox was already not a restriction.
- If you get more air and more fuel, you get more power and therefore you let off the gas pedal.
I doubt that covering or leaving the holes would change anything, unless it affects intake air temperature.