I just discovered this post and decided to give it a try on my LC 475. It was a success so far!
I just moved the resistor to R95 (didn't replace the MC88920 chip) and with a full 25MHz 68040, it was pretty stable at 40MHz. I joined my home network, browsed the Internet, downloaded, decompressed and copied some files, ran some benchmarks along with modelling and rendering with KPT Bryce for around two hours with no major issues.
I just had a few issues when changing the frequency on the fly. I first experienced a freeze of the system and a crash of the Finder another time when shutting off the Mac. However, when rebooting to the same frequency without changing it at any point, it seems to make everything pretty stable. I will see how it goes with time.
Not sure if I should invest in a proper 40MHz CPU? Such a bump in frequency may be a bit tough for my 25MHz chip?
Amazing discover and amazing job anyway! Thank you so much for the awesome work! My dream of having a 68040 machine @ 40MHz has come true!