Does a 03 TL-S have some sort of protection when the motors not fully warmed up? I was leaving work and had to merge into traffic. I got on it and it seemed to shift early and shift out of vtec. But seemed fine later on down the road.

 

As a safety - the trans is programmed to hold lower gears longer while cold to help warm itself, and it will feel as if shifts a little rough for a few minutes.
After a few minutes its warm and trans returns to nomal
If cold there may be rev limit for same reasons

 

VTEC will not engage until the engine reaches a certain temp. So yes it does have some kind of self-protection. You should always keep it below 3k before the enigine warms up.