i'd open that up also.
when i had my tmoss ported lower with my old combo. i used a stock upper. i just opened the stock upper up to match my 70mm TB, and blended it back as best i could... 10X better than having a step for the air to hit and cause turbulence which slows airflow.
the stock intake goes from a circle and smashes into a tall rectagle to clear the middle bolt holes holding the upper down. not much you can do with a stock upper unless you can do besides work on the TB inlet side and port match the upper-lower holes, or you can cut it apart and port on it and weld it back together. but according to Tmoss, the stock upper isnt really a restriction and works well with a ported stock lower.
upgrading a TB on a stock headed, stock intake stock MAF car isnt going to do much, first off the stock MAF is smaller than a stock TB, even if you had a bigger MAF and TB, the stock intake and heads are the real choke points before the TB. but it sure does look like the stock maf meter is a big choke, its pretty small.