I've done parts substitution on equipment for a long time, generally don't mess with values, these values designed to meet circuit criteria. I generally stick to changing out with higher quality, closer tolerance, same value caps, resistors the same. Higher voltage caps than stock generally ok. As for Coincident products, having Israel change out volume transformers, installing Amtrans selector, changing out PS caps on my Statement pre was nice upgrade. I diy changed out a few caps in signal path. On my Turbo 845SE haven't changed a thing.
Transformers and power supplies critical in tube equipment, I'd contact Israel and ask about possibility of mods you're contemplating. Israel has been fine with me working on my Coincident, I simply related my longtime experience with soldering and changing out parts.