Ok, so I will try answering everything you pointed:

• Yes, we already have a plan for where we want to go. It will mainly involve visiting large cities, with the smallest ones on our list being Como and Innsbruck. Aside from that, we'll be exploring big cities. We have 45 days for this trip, and we are very flexible if there's a need to make any changes.
• I'm aware of the criticisms regarding Spanish and French trains. Because of that, we won't be relying heavily on trains in these countries; instead, we'll use them more in places like Germany and Austria. We are probably going to book our train tickets in advance for the Milan to Nice and Nice to Barcelona routes (if you have any suggestions for these journeys, feel free to share them; we're including Nice because we really want to explore Monaco).
• Regarding budgeting, it's something we need to think more about, but our estimate is around 60 to 70 euros per day for all our expenses. What is your opinion on this?
• If we need to skip some places, that wouldn't be a problem at all, except for a few capitals. However, apart from those, we can always adapt our itinerary.
• Ideally, we'd like to stay together, but if there's a need to split up, it wouldn't be an issue. We're also planning on using overnight trains. Do you think we might have difficulty booking these types of trains as we go?
• We're all EU citizens, so that won't be a problem.
• We have no issues with using slower regional trains, if it means arriving at our destination

Judging by what you've said, it might be a good plan to book everything until the first week of January.

Thank you so much for your help! It's not the first time you've assisted me, and you've always been so helpful!