It is definitely time to get a new tune. KOJO will correct that code and mention it anyway when going over details of the behaviors that you want.
Keeping the old tune will work, but will also keep the system out of balance and waste the turbo's potential and your fuel. The ATT's characteristics (amount of fuel and injection timing at different loads) are different than other turbos and the correct tune (from KOJO whom got it from ATT) will bring the system in balance.
If you already have an ECM with KOJO's tune, go ahead and swap it out
In terms of simply swapping out the ECM's, Yes, it is that easy. Just take your time and do not force the connectors. Also, KOJO's recent instructions call for having a warm engine (above 180F *AFTER* completing the swap).
Toward the vacuum system, I simply removed the vacuum pump (actually it had just died, so I had an excuse) and left the other parts alone. I also got a new tune that allowed for the vacuum delete at the same time so I never got the P1656.
Also, reminder that removing the vacuum pump calls for a different size belt (IIRC one inch shorter). Best to search a bit for your year truck to see what length others used. Another way to go is buy several belts, install until one fits well, and return the rest.