I think the key piece of data you're missing is the correlation between the old RGYB telephone wiring standard and the newer cat-x convention:
1st pair, usually for phone line 1:
2nd pair, usually phone line 2, if used:
Third pair, if present (looks like they exist in your photo):
If it makes sense in your rewire, you might consider just leaving the present phone service on the existing RGYB quad wire. Use a 4 way keystone wall plate, and terminate the 2 new Cat-5 wires on RJ-45 (4 pair) jacks. Then terminate the existing daisy chain phone line on a 2/3 pair USOC RJ-11 type jack just for the phone. You'd want to use wire nuts to tie all the reds and greens together and add short stub pieces of the solid wire to actually punch down to the phone jack, as they don't take multiple wires well. If you want to carrry the 2nd and/or third pair through, you'd do the same with them, but that junction box might be too small to fit all the wire nuts comforably. That way you'd have 2 "data" jacks and 1 "phone" jack on the wall plate. The 4th hole on the keystone plate would get a blank for looks.
If you're moving the phone service over to one of the new Cat-5 wires, just punch down all blocks and jacks 1:1 with the primary incoming phone line connected to the blue/white pair at the source as motox suggested and it will work fine. No harm in also punching down the 2nd pair to the wall jack in case you ever need a 2nd phone line. Use a 2 port keystone wallplate, with one RJ-45 jack for data and one RJ-11 type for phone (whose unused 3rd and/or 4th pair are just folded back out of the way).
Hope that helps...