|To answer your question, yes, a 100 Mbps connection only requires 2 pairs so you could break your cable as you suggest.|
Here's how it's done:
Pay attention to the following section:
Cable and Connector Pinouts
You'll need to punch wires #1, 2, 3, and 6 correctly into both RJ-45 ends. The listing for all 8 wires is just below.
I have an alternative suggestion for you. One I personnaly consider a better option if it's viable. Use the existing Cat5e cable to pull a couple more cables through the raceway.
It matters not how straight the gate,
How charged with punishments the scroll,
I am the master of my fate;
I am the captain of my soul.