I heard that you can remove the secondary butterflies in the throttle body. Does this work? how does it help?

 

Here's a good link

It's also in the archives...

 

its been forever sice ive seen that faq in its entirity

 

There are two sets of secondary throttles. One of those sets (the upstream one) is held closed until the engine warms up. On Turbos (but not NA's) that set has a damper that slows there opening rate to smooth the transition as the secondary ports start to flow. These can be removed.
On Turbos removing them improves throttle response. On NA's it has very little effect, because they're not damped. The only benefit is the removal of the minor restriction posed by the open plates.

 

TB mod on an NA...
Cons: Cold starts on cold days takes some pedaling to get warmed up.
Pros: Eliminate the fails-by-surprise coolant line.
Easier, faster access to upper engine stuff.
Minor HP gain, Minor throttle response improvement.

 

Removing the thermowax isn't necessary. The #2 secondary throttles are a totally seperate system that can be removed without affecting cold-idle.