My thought on the subject(maybe wrong) if you are using the stock efi it won't matter too much because the stock efi runs the injectors in batch. However, if you are using a standalone you may have to get them to open on earlier as kid has mentioned.
As far the plate goes I believe the stock flange is something like 10mm. So, it wouldn't be that much further away than if you were to leave it stock, however the 1/2in is still bigger than the stock flange.
Why not places the holes on the flange and eliminate some headache or heartache.
Also you have to make the intake flange thickness match the exhaust flange thickness otherwise you will get leaks(vacuum, exhaust or both).
Hope this helps. I've maybe not ripped apart as many as some people here, though I've read enough and done enough stupid things to not listen to people who have been there before me.