Trouble with a 3-way circuit

I'll try to be as specific as I can here. Thanks to anyone who can give me some info.

My wife wanted to replace a set of 3-way light switches we have in our hallway. When I wired up the new switches they didn't work correctly.

Here is the situation: Power from the box comes into one switch box in the hallway (2 wire line)(may not come directly from box, but is definitely the power supply). From here the Neutral wire on the 3-wire line is connected to the hot wire on the incoming 2-wire line (white to black). The Neutral wire from the 2-wire line is connected to the switch as is the black "hot" wire from the 3-wire line and the red traveler. The second switch is an end of run, all wires are tied to the switch.

Here is what throws me. After taking out the fixture, I see 4 pairs of 2-wire lines tied together (none of these have red travelers). One line has a neutral wire spliced directly to the fixture, the rest of the "white" wires are spliced together along with a "black" hot wire that runs to the fixture. All 4 of the "black" hot wires are spliced together.

So what I am thinking, because I don't see travelers spliced together in the fixture box, is that Power comes to the fixture and is then run to the first 3-way switch, where the neutral wire from the 3-wire is spliced onto the hot wire from the 2 wire run. Then the 3-wire is run to the second switch which is the end run. I have no idea what the other 2 pairs of wires are running to.

My only thought is to undo where the Neutral 3-way wire is spliced to the hot wire and splice the neutrals together while attaching the 2 hot wires to the switch. Or will that royally screw this up?

TL;DR 3-way circuits are confusing as fuck and whoever wired this house in the 60's was a maniac.

Submitted November 30, 2014 at 10:51PM by madasser03 http://www.reddit.com/r/DIY/comments/2nutwy/trouble_with_a_3way_circuit/