If you want to do all this, honestly, I would go for the ATP Turbo upgrade, since you do have cores you can send in to cover the core charge. The main weakness in the OEM turbos has been the seals, and I believe they address that in the ATP upgrade, but you should doublecheck with them. The advantage is simple, same power at less boost, or more power at same boost. Less stress on your powertrain, if you so choose.
New OEM turbos are about $500 apiece, and will come with 2 yr/unlimited mileage warranty. You will still have to return your old turbos as core. This is the better way to go if you do decide to swap out for the Fusion.