If I am reading the Electrovibe schematic correctly and matching the corresponding transistor in the Madbean schematic, Madbean's Q11 corresponds to Pedal PCB's Q1/Q2.
So, you'd insert the rate LED and corresponding resistor to LFO Out on the Analog LFO block on the schematic. Seems like the middle lug of the Speed 1.1/1.2 pad is the logical place and then run a wire to ground with the resistor. You may want to tie it to the Effect bypass switch so that when you switch it off, you also switch off the Rate LED.
Interesting stuff. I was going to forego this as I thought it would be more difficult but it seams I'll have to factor this in to my build.