Howdy So I came across those two components which can solve our positioning problem with the wafer:
Those LEDs produce a light within the spectrum we need in order to shine through silicon (1000nm ~ 1400nm): https://tech-led.com/en/product/ir-nir-leds/
The OV5647 is sensible up to at least 1000 nm and is quite affordable: https://cdn.sparkfun.com/datasheets/Dev/RaspberryPi/ov5647_full.pdf
There are OV5647 imaging modules available for Raspberry Pi. I'll try to contact Marubemi directly and ask them for a quotation on their NIR/IR LEDs in the wavelength range we require and while I'm on it, I'll also check with them for a potentially more suitable CMOS sensor, then I'll compare the prices. As I've discussed with Dilek, the goal is to produce an affordable stepper suitable for hobbyists and small labs with limited budget.
Cheers David