I have a 2011 GT, while it is now supercharged, even in stock trim was a blast to drive.
I also have a 2014 Focus ST with a Eco Boost engine. It has upgraded intercooler, intake, cat back, and a tune. While it's a fun car, and the eco boost is a good engine, don't think I would ever order a eco boost in a mustang. If you really get on it, it's a lot of fun, but on the highway, or when in higher gears, no where near the torque if the 5.0
so if I had a choice 5.0 all the way
^ This. Depends on whether you want 'peppy,' or powerful.
Personally, I'd be very worried about mods and warranty on any turbo engine. I can't imagine Ford looking the other way if you've altered boost PSI, or swapped out the turbo for an after market version. Additionally, I'd budget for the extended warranty on an EB car of any kind. Not necessarily for catastrophic failures, but even for the multitude of sensors and electronics involved. And, this EB is new for Ford.
Marrying this particular engine with a heavier convertible model means it will be a little slower than the coupe. Ford has also geared the convertibles on the weak side in the past, too.
I know you want that appearance package, but I'd be darn sure I got to drive THE model I was ordering before I ordered. Only thing worse than paying more than you feel you can afford, is not being happy with a 35k major purchase, then taking the depreciation hit to get something better.
I'm very interest in the EB myself. But, if I get one, I won't be modding the engine until I decide warranty no longer matters.
Perhaps you should focus your mods on remaking the Anniversary appearance, and getting the body and engine you want from the factory...