Hi,
Fantastic ! Do I envy you with these 12 weeks or so for a trip!
Going over without stopping in England and focusing on west and east central Europe for almost 90 days (just make sure it's an exact count...no big deal anyway, I 've never had problem keeping track of it), I would plan my trip taking full advantage of (1) night trains using the Pass, (2) ferries, (day and overnight), esp if the 30-50% discount can be applied by using the Pass, if you're going to Poland, Sweden, Serbia, Norway, Germany, Finland, (3) the various bus companies ,ie using the combination of train and bus, using bus night routes, (4) the discount air carriers (sparingly) depending on the geographic extent of the trip
With this extended time frame, my itinerary would include after landing in Copenhagen (2-3 nights), Finland, Poland, Germany, Hungary, Austria, Czech Rep, France, Austria, northern Italy, , Kleipeda (Lithuania). Logistically, it can easily be done if you know what you're doing, plan and reserve ahead, use the trunk lines for day trains, use night trains to squeeze out extra time, pace yourself, focus on train schedules, and buses too if you're using them.
Since the Global Pass includes Poland (it didn't use to), you can go from Cologne to Warsaw by night train, direct. That route in the opposite direction used to go as night train Warsaw to Amsterdam, now it ends in Cologne....makes not big difference anyway.
I would not necessarily wing it when it comes to taking major train lines, since if you tailor the route you may transfer less often, say once as opposed to 2-3 times, getting from A to B. That requires planning, plus getting more for the Pass.