Did you disassemble or dismount the hotend during your modification? I once did some work on the extruder/hotend of my i3 clone and the wiggling snapped off one of those tiny thermistor wires, after that my printer read some weird and whacky temperatures as well. Check the connections at the thermistor to see if the wires are still intact and not fraying or partially broken.

A thermistor that changes temperature as it heats/cools, but the point it thinks of as room temperature is shifted sounds like something has happened to the resistance of the circuit. This could be a few frayed strands of wire, a dodgy connection. Or if you changed your firmware you could have the wrong thermistor table loaded.