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.
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
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.
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.