I'm not really in a position to suggest an "ideal route," but I'd say don't miss Meteora; it's one of the few truly unique sights, available nowhere else in the world. Judging by my transit through there less than a month ago (late October), it's probably very crowded during the season.
You already know Montenegro and Romania, two of my favorites, so I suggest going for Albania; it's much more rough around the edges, which I take as a good thing, and in places fairly rugged. While there, stop into Kosovo just for the geopolitical glimpses (and friendly people, often-stunning mountain scenery, relatively untouched monasteries, etc.).
You don't say what time of year you're looking at, but I'm assuming if you're riding the Italian Alps you probably mean summer or early fall. Albania in November can get pretty gloomy, as I discovered last year. Early October would probably be just about right; three weeks ago there was snow in the air everywhere, and the winter storms were moving into Italy in particular.
Hope that helps.
Mark
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