I have been in the same via crucis, have followed all these links (specially http://wiki.makerbot.com/forum/t-303275/so-close-to-first-print-but...) and still nothing.

Sometimes, specially when I cold start the bot, the toolhead is found and works for some time. Then, usually before I can print anything, the ReplicatorG stops showing temperature data and any operation involving the toolhead returns an error. However, the EC keeps controlling the temperature, turning the relays on and off and everything.

Moreover, even thought I don't have a logic analyser, I traced the signal from the EC to the mainboard using ans oscilloscope - TX and RX in the EC, A and B in the 485 connectors and RX and TX in the MB. Data flows both from the MB to the EC and back from the EC to MB, but the MB still reports the toolhead as missing.

I'm in the same boat. I started getting the same error last night and I'm absolutely stuck. It quit on me just as I was about to start a test extrusion using the repG control panel; the extruder stopped and temps dropped to zero. I unplugged everything, switched patch cables, downgraded firmware on the EC and motherboard, and checked the power source. The EC works--I can still get it to operate the extruder, extruder heater, and HBP, but I can't get any temperature readings. (Both the extruder heater and HBP read 0.) All lights on the EC are green. Same setup as original poster. Please help.

Same problem.  I have managed to print by editing the G-code ReplicatorG creates.  I remove the part where it waits for the head to heat up and the test extrusion.  Otherwise it would stall waiting for the head to heat up because it can't read the temperature.   

One last thing.  I downgraded the firmware to version 1.6 and it detects the toolhead and shows the temperature BUT I get some error saying it couldn't parse or interpret the g-code (not sure of the exact wording.)

I'm not sure if this helps you but it is a good thing to check. My ftdi cable was broken out-of-the-box. The ground pin wasn't even soldered in, so after a few wiggles it was out and giving me erratic behavior. I definitely got the toolhead error. Check out your connections there. Swap it out if you have another, or just make sure all of the wires seem secure. I soldered my pground and then zip tied it to secure it and prevent it from stressing when I move my laptop.

Another weird one was that my computer needed to be plugged in for whatever reason (grounding possibly?)

Good luck!

same problem here, no more communication to my extruder controller :(

Even without updating firmware or replicatorG, the problem vanished as suddenly as it started. Which is worrisome.

A few weeks ago I got stuck in a loop where I could connect for a short period of time, then I would get the Toolhead 0: error. It eventually went away after reflashing the toolhead firmware 20-30 times. I have since then noticed that the toolhead will become unresponsive to temperature settings after running for a period of time. Usually a restart of repg and a shut down of the bot will cure this. No idea if they are related to this problem, related to static electricity, or what.

Check the resistance of your DC motor. I found that mine had a short in the cable, which crashed the extruder controller whenever I tried to operate the extruder. The temperature reading in ReplicatorG would drop to zero, and I'd lose control and get that error message until I reset the controller. Even with an OK cable, I've read the DC motor can occasionally short in some positions and cause a matching crash. There are H bridge designs on Thingiverse using transistors and MOSFETs to insulate the board from this problem. 

I fixed my toolhead not found problem. After weeks of trying everything I finally fixed it and I am posting what worked in the hopes it will help others.  I tried firmwear updates all of them every combination. I tried cutting the reset. No luck. It was a brand new EC board. I could talk to the EC board over USB but not through the motherboard/eathernet to the E C boardto update firmware ect. It was like it couldn't talk to the EC board while going through the motherboard/Arduino1250. after trying muliple eathernet cables of differnt lenghs ect. I was about to send the EC unit back to have it tested/replaced and while I had it apart I decided to try one more time.  I had read in one of the group posts somewhere that some arduino's were not updating properly whitout taking the motherboard shield off.  I know Makerbot says not to do this. but my next step was to ship it back  so I figured while I have it apart?  What did I have to lose? So I took the Arduino off the motherboard sheild. updated the firmaware pressing the reset switch on the arduino board and it seemed to update.......It was working?  It couldn't be that simple? But it was,  I put it all back together and it worked on the first try. Now here are my thoughts One does the reset switch work on the sheid/motherboard the way I thought it did? Does the reset switch on the motherboard  reset the Arduino? Or when the reset is cut on the Arduino is it somehow making it so the reset switch on the motherboard sheild not work anymore somehow? If you try this and it works please post so others will know.. Maybe I just got lucky. All I know is by updating my firmware on the arduino while the sheild was off suddenly things started working for me.  When I put it all back together no more errors.  I could see the temperature being updated in the control panel the graphs were working. I am using Generation 4 electronics and Repicator G (V0025) with an ardruino 1280, Motherboard 2.6 (V2.81), Extuder contoller 3.6 (V2.8),  Thingomatic with heated build platform firmware,