What Chris said!
This is your centre pipe with the exhaust valve:
While this is the 696 version, which is straight through:
You may well be able to pick one up from a breaker, (pt. no. 57211491A), like this one for about £50
https://www.ebay.co.uk/itm/Ducati-Mo...3/133223784458
Regarding the reflash, it should smooth out after a couple-of-hundred miles but bear in mind, as I said earlier, the 796 has a lightweight flywheel, which doesn't help low speed running.
As for the forks, you can't go wrong with either K-tech or Maxton. They both really know their stuff and have great customer service. My forks are now a K-tech/Maxton hybrid so I've had experience of both.
Keep us updated on all your mods!