How to troubleshoot home thermostat wires

Haven't hit the Google yet but I figured if post here to give you all some time while I Google.

I need to fix my thermostat wires. In my house we have a very cheap non programmable thermostat. I got a nest for Christmas. I went to install said nest last night and was happy to see 5 wire thermostat setup already in wall. Bing bang, unhook old, hook new, zero dice. Wft? 

Now the fun starts. I go to the furnace and see that what was a white sheath 5 wire cord is now a brown sheath 4 wire cord. And a separate brown 2 wire cord is also connected to the furnace but looks like it probably goes to the AC unit. Great. So somewhere in my wall (no conduit, like I'm pretty sure is necessary per code here as well) there is a splice between the white sheath 5 wire and the brown sheath 4 wire. Quality.

So, not all is lost because the nest says it can run on a 4 wire. But, in the past with my thermostats I have known that to mean the thermostat does not have fan only control, which is sometimes kinda nice. I'm pretty sure the current setup only works because the dumb thermostat uses batteries for power and not the red wire from the furnace, which looks hooked up but I bet isn't.

Should I attempt to just pull a new 5 wire all the way? Should I attempt to find what is connected to what (hard because there is a full set of stairs in between, but I guess I could use another long wire and multimeter)? How can I test if the 5 wires at the thermostat end are at correct voltage to rule out a faulty nest (which seems unlikely, but you never know)?

Ok, now I'm pretty sure I have nothing to the common wire, but the power, fan, ac, and furnace wires are correct.

So at least that is a start.

Would you look at that. If there is no power to the common wire, and you hook it up to nest, nest will not turn on because the common is off. But if you just disconnect it, nest turns on without it. Which makes sense.

But also means my common wire is not simply disconnected at the other end somewhere in the wall, it means it is connected to something that isn't common power. Or, it means the nest is smart enough to sense a wire plugged into the connector and not just the signal from the wire.

How many feet of wire between the thermostat and furnace? That is to say how hard would it be to pull new wire? 

My suspicion is the splice can't be too far away from one end or the other because lazy people aren't usually half-assed about their laziness.

I had a 4-wire from the furnace to the wall, but the installer stripped back the +24 wire and wrapped it around the outer jacket and stuffed it into the wall. I easily pulled out a couple of extra feet of thermostat wire at the thermostat and had what I needed for my Honeywell Nest clone.

That was after I opened the furnace access door and saw the wire similarly wound around the jacket.

All that said, I have an unfinished basement so it was pretty easy to see where the wires go.

I pulled as far as I could from the thermostat side and didn't get to the splice. The house was a flip and I fear they spliced it before they redid the drywall in the storage room ceiling. However, it does seem that the nest is now working without the common wire, so that is good. 

I learned the easy way to test the thermostat wires however! 

1. Jumper red to green = turns on fan

2. Jumper red to white = turns on furnace

3. Jumper red to yellow = turns on ac (don't connect and disconnect and reconnect though, that can damage the compressor, always give 5 minute cool down time).

My "yellow" wire is actually blue, but the ac does work in the summer so I'm guessing that is just more lazy splicing.

Apparently looks like for now I don't need to pull a new wire, so that is good. If I need to though, I think it will be possible.

I've got heat and A/C with only 3 wires on my thermostat.  we are lacking the manual on for the fan because of it.