Yeah, the final act of the final zone is the low point of the game for me. It's the only level in the ENTIRE SERIES where I've timed out.
The boss is awesome though.
One of my favorite level in perhaps the series. If you timed out you were going to slow and the level challenges arent that hard. Just keep the pace up. I thought it was a mistake they stopped the time at the boss though, but i can see why.