Yes, strip off the rj-45 connectors from each end. Put 2 or 4 (depending on the phone cord your making) into a phone-line connector and crimp it. Then put the same color cables in the same order on the other end into a phone-line connector and crimp it. The excess wires can be trimmed so they are not hanging out of the cable.
In a RJ-45 you will use any two "twisted pair" of wires. There is polarity (ie. red/green) on conventional telephone cords. You just want to keep those the same at each end and you will only be using the two INSIDE contacts of the plugs.