It couldn't hurt to try a different insole. I use SOLE insoles in my road shoes. This may sound out there, but I also have a bit of moleskin that is attached to my insole. I've long had a bad hot foot (well, really it's a hot toe) issue. It doesn't really matter which shoe I wear, although my SIDIs are not the top of the line so I can't say that I've exhausted my options. Between better insoles, the moleskin, thin socks and the repeated use of Tiger Balm during the course of my rides, I can keep the pain mostly at bay. Prior to these admittedly weird fixes, the pain would be about a 9 on the pain scale. The fact that you didn't previously have any issues and have otherwise replicated your cleat set up has me stumped though. That stinks.
Live with intention. Walk to the edge. Listen hard. Practice wellness. Play with abandon. Laugh. Choose with no regret. Continue to learn. Appreciate your friends. Do what you love. Live as if this is all there is.
--Mary Anne Radmacher