There is going to be a difference in performance between swapping forks onto a bike and getting forks engineered for the specific application. Any problem can be overcome if you throw enough money at it. Spacers can be made, axels can be turned. The valving and spring rates are unlikely to be correct and will have to be changed.
Have you though about buying Ohlins internals for your forks, very common in supersport where the forks must remail externally stock, works well. It will be more expensive to purchase but will likely save money in the long run.