There is only a little bit of work to do with those lumps. Remember, they have to be pulled out to perform porting, valve size increase and new guides, ect. When they are out, just have the guy remove a little from the bottom of the port so they sit flat. Not a big deal. That is why the bolts were not cut yet.
You only wanted me to do some of the work.
Tom, if you don't mind me asking, why would you "only do some of the work" as far as the lump? Is there not a set procedure? Just trying to learn here. Sorry OP.