E3D upgrade in an unknown printer

Hello

I have a Joysmaker R2 (it's a chinese copy of the ultimaker original but with heated bed and display with controller, and I changed the hotend to the E3D (on this link [www.aliexpress.com] )that uses the 104gt-2 thermistor (number 5 in marlin's list). My pcb had to be replaced too, I installed an ultimaker 1.5.7 pcb.
My problem is that the original hotend used a thermocouple and the E3D used a thermistor, now it is showing max temp error because the nozzle temp is showing about 500 celsius, but it is working because if I heat or cool it manually the temperature in the display changes accordingly. So I came to the conclusion that this is a firmware setting problem, but how and where can I change this setting? The only firmware the seller's website is the cura instalation that comes with the .HEX file which I can not edit.
I found a website that builds the firmware if I have all the configuration data and specifications, but I dont know where to find this info. I tried to Build one anyways using default configuration and used the 104gt-2, then when I flash it the printer reboots showing the right temperature but then the software in the printer freezes and I cant do anything.

Any ideas?

Edited 1 time(s). Last edit at 05/24/2016 10:40PM by wjuniorbr.

It will be much simpler if you just purchase a thermocouple with a m3 threaded end and screw it in the place where the bolt holds the thermistor in the heated block.

But your pcb might have a connector for the thermistor, if it does just change the type in the firmware.

Edited 1 time(s). Last edit at 05/24/2016 09:01PM by ggherbaz.

I could, and although this board needs an additional board (amplifier), it would work with a thermocouple, but the thermocouple in this printer was one of the reasons I wanted to change the whole hotend, the old hot end has a thermocouple, which I tested and it works, but the interference it receives is way too high for me to go back to thermocouples. Whenever I started a print it would heat up as it is supposed to and then as soon as the axis or extruder motors started the temperature reading fell about 20 degrees(sometimes more sometimes less) and the printer would continue to heat these 20 degrees, in the end I was always printing somewhat 20 degrees higher, I use to offset a little by choosing a lower temperature, but doing that created other problems too. So I reeeeeeally wanted to make it work with the thermistor, I heard the interference is close to nothing and that would be a dream to me.
But thanks for the idea, keep them coming.
Any chance I could extract the current firmware from my arduino, then edit, and then flash it back?
I also have the .HEX file of a marlin with my machine settings, is there a way to convert the .hex file to the usual set of files that makes the firmware, then edit and then flash it back?

Edited 1 time(s). Last edit at 05/24/2016 10:31PM by wjuniorbr.

I have seen the hex converter before, let me find it and will let you know soon

Ok thank you very much

Here you go:

[www.google.com]

[www.google.com]

You will edit the hex file itself and the flash it back to the board.

Thanks again