Ported the S5 Turbo wastegate as I am going with larger intake and exhaust. Unfortunately ported a little too much and now it is not sealing. Is this a big issue? I can still build it up and fix it while it is apart.

 

You are letting exhaust gas by that would normally be used to spool the turbo, so the only downside is a less responsive turbo. Can't give an estimation as to how significantly though. As long as the housing structure is not weakened, I don't see how reliability would be affected.
You can also weld washers to the flapper door to cover the larger hole. That's the route I went with my S4 wastegate.

 

Did some searching and it looks like as long as 75% of the hole is covered I am good. It will add a little lag, but it will further aid in preventing boost creep. I am trying to build up the flapper to cover the hole. If that doesn't work than I will just leave it.

 

Might as well do it right. Pull it apart and make a new flapper. You should also cut the corners inside the hotside to help flow to the wastegate.

 

You'll be fine.

An open intake and exhaust easily compensates.