Add an IR sensor control to existing machine control code

I posted a job about five months ago and hired someone who wrote some excellent code to run a machine I built. But now we are having a problem. This machine incorporate two mass flow controllers. One for propane control and one oxygen control. This produces a flame that is employed to heat glass tube to a malleable state. There are a number of stepper motors which drive tools which form or shape the heated glass. Initially I chose a thermocouple to monitor the flame but I feel the reaction time is too slow. Therefore I have opted to switch to a IR sensor to monitor the flame and shut down the machine should the flame go out. But we are encountering a problem. For some reason this person I hired to write the code and myself working together are unable to get the IR sensor working in place of the thermocouple. This is why I am posting this project. I would like to hire a third set of eyes and expertise in writing code to help us resolve this problem. The machine is run by an Arduino Mega 2560. If you are interested in helping us resolve this issue and you believe you have the expertise required to make a meaningful contribution please contact me. Attached are some images of parts of the machine from my original project posting. All inquiries welcome. This would probably be an hourly project.