That sounds like an amazing trip, I am jealous.
In terms of route: I would aim for southern Switzerland, the famous Grimsel-Furka-Susten triangle, and then on to Liechtenstein and Austria (you can find a cheap hostel just across the border in Feldkirch), then down to the Grossglockner (I had a good experience at Hotel Mölltaler just past the southern exit).
Then you can drop down into the Italian Dolomites, stop for a cafe e gelato in Tolmezzo, and take the SS13 and SS54 to Kranjska Gora - stay there overnight and do the Vrsic Pass the next day. (Alternatively if you want to do it from the south, SP74 from Chiusaforte takes you up to a small border crossing and was amazing in itself.) From Triglav National Park, most tourists would go east to Lake Bled, but I would recommend you follow the Soca valley south - through Idrija and on to Postojna with its amazing cave and nearby Predjama castle.
Once in Croatia, I would head for Plitvice national park - lots of guesthouses in the surrounding villages, and definitely check out the ruins of the Plitvica air base! The island of Pag just north of Zadar is a very unique experience in itself (take the mountain road from Plitvice to the ferry at the north end of Pag). Then head south on the excellent Croatian motorway - Split has its charms for sure, but you can skip it if you've seen Zadar.
From there, I would follow E65/A1 into Bosnia & Herzegovina, particularly into Mostar, and stop at the Kravica waterfall on the way - it's unique among a number of similar locations (e.g. Krk in Croatia) in that at least last year, they actually let you swim in the waterfall by the bottom of the pool.
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In Mostar, go on Sheva's free walking tour!
Then you'll hit Dubrovnik - well yes it's a tourist trap, but for a good reason, the Old Town is really awesome, and I say that as someone who grew up in an old Hanseatic city! Heading down into Montenegro, take road 516 via the Vitalijna peninsula for a much more pleasant ride, bypassing the frenetic border crossing on the main road. Kotor is very pretty but really a smaller version of Dubrovnik - stop for a small walkaround, then head up via the Kotor Serpentine into Lovcen National Park and the very charming old capital of Cetinje.
That's as far as I got on my own travels - headed back via the completely un-recommended Budva
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With your destination in mind, I would keep going down through Albania and North Macedonia to Bulgaria and onto Turkey.
In terms of Istanbul... obviously the traffic is going to give you a major headache on a bike.
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But the city is amazing. You will have read about the obvious sites - the palace, Hagia Sophia, the Galata Tower - but my two non-obvious recommendations would be to take a (foot) ferry out to the Princes Islands, and a cruise trip up the Golden Horn.
On your way back, you will probably want a faster highway trip - so through Bulgaria and Romania, where the obvious magnet is the Transfagarasan Pass (and the slightly less amazing Transalpina), but I would also recommend the Semenic-Chenei national park in the west, and the Turda salt mine, Brashov town with the nearby Bran Castle, and Cluj-Napoca as a highly charming town in which to stop and walk around. Then just follow the highways to Budapest-Vienna, or into Slovakia via the Lower Tatras and Prague (for a good riding alternative, go via Usti nad Labem and Hrensko, check out the Pravcicka Arch and Bastei before getting into Dresden). Then you can head straight west across Germany, do a lap of the Nürburgring, and then you're within spitting distance of La Manche.