Our original route before we decide how to get to Istanbul is to get across Europe using mainly the Eurovelo 5 and 6.
We started our journey by taking the Eurostar from London St Pancreas to Lille France. You can ride to Dover and take the ferry across, but we actually found this option to be more expensive and a lot less convenient. The Eurostar has a bike carriage that you can drop your bike off at 24 hours prior to the journey with your bags and then you pick everything up at Lille station.
We generally stuck to the Eurovelo 5, excluding Brussels, and we picked up the Eurovelo 15 to ride along the Rhine for a short time out of Strasbourg. You can ride on to Basel on the Eurovelo 5 (this is by far the easier option) but we wanted to go through the Black Forest, this option does take you up a 1200 meter climb, but it is an amazingly beautiful journey.
We then picked up the Eurovelo 6 at Donaueschingen Germany and have stayed alongside through to Serbia. Excluding some times in Hungary and Serbia when the route has been uncrossable and we have had to make rash decisions to find alternative roads.
Based on time constraints and our eagerness to get to Istanbul we decided to travel across Bulgaria, over Shipka pass, to Erdine Turkey. From there we travelled southeast to Gallipoli. After crossing at Gallipoli we travelled back west and took a ferry into Istanbul from Banderma.
This route took us on some difficult main roads in Bulgaria and the climbing was challenging through the Balkins (but it was only about two days of serious climbing). We chose to take a long way round to Istanbul and entered via a ferry because of the difficulty of the highways into Istanbul.
I would highly suggest this route but it should be noted that the ferry into Istanbul was expensive (approx £20 each).