My intake holes are a little off from my cylinder head. Is it worth the time grinding it out or just leave it? Maybe try and make the air flow better by rounding off those edges. It's a bare intake so no worries about shavings getting into things. Suggestions please.

There shouldn't be any issue, providing you've got enough intake stock to handle the reduction in mass. There may be a penalty in fuel/air distribution, however.

It's been proposed that having the intake side port slightly smaller than the head port provides some anti-reversion benefits. Keeps the charge from coming back out of the hole. From what I've read, the real restriction to flow is inside the head, so it might not offer any benefits. Lots of good reading over on Hybridz.org. Look for BRAAP's postings.

It's not really clear what you're showing in your picture (to me anyway). How did you determine that there was a mismatch?

I had some gasket material, that dark gray stuff, that I laid over the port side of the head and tapped out an impression with a small rubber hammer. Then with an Exacto razor knife cut it out and and taped it to the intake and saw the difference. I have read some info off hybridz about the restriction being inside the plentum of the intake. The square exhaust ports matched up perfect with MSA's 6 to 1 header. I don't have the bigger throttle body or anything other than the header. I was thinking (big mistake) that just rounding off the edges or "flowing" would help get a little smoother air flow coming in the head but maybe I'll just leave it be. I'll read what I can find out there. Thanks for your replys.

My intake holes are a little off from my cylinder head. Is it worth the time grinding it out or just leave it? Maybe try and make the air flow better by rounding off those edges. It's a bare intake so no worries about shavings getting into things. Suggestions please.

Don't bother, unless a head port is blocking off an intake port (opposite of your situation). Unless you plan to hog out the rest of your intake to match, you're not gaining anything.