I have an 04 Speedmaster and did the same airbox mod as you've described in your post. I have 140 jets installed on the bike with stock needles/shim and have not drilled the vacuum holes. I have not experienced the surging you've described. I'm about 3 turns out on the screws. Hope this helps.
So perhaps the needles are the root cause of the surging? I'll defer to the experts.
BigSteve
