yes it will make a big diff, you lost all the intake air velocity. just like you said with the big gulp of air and the straw, the air is just blowing around in your mouth and it slows down alot.
just like you want exhaust velocity you want intake velocity too. you want that air to go in and out as fast as possible.
thats why a bigger TB is one of the last NA mods to do. get a nice header or port out the stock manifold and a nice freeflowing exhaust and some cams and then you can take advantage of the bigger TB.
Thats how I started out too, I got most bolt on's and was pissed cause my car was slower that stock, now that Ive got all the mods to back that TB up its much better.