If its been running fine with that hole in there it means that its probably over fuelling now you've patched the hole.

If you have an air leak thats not going past the metering head on the MFi system it will lean the mixture out, sounds like yours has had the fuel to suit it with the hole there.

I would defo take it to a garage and get te h base mixture tested at the very least, then maybe to a rolling road to make sure the fuelling is ok right through