The CANBUS issue can be resolved by the proxy alignment protocol if you have the right software and cable for a laptop, so it isn't the end of the world.
You would need to do ECU etc etc for a 2.0 though.
Honestly, I would stick to putting a 1.6 in it. Insurance companies get a right hard on when they hear of engine conversions and will happily stiff your wallet for the pleasure and selling the vehicle on with an engine conversion will always be harder work you'd probably not see your money back.
the 1.6s are a good strong motor with 120bhp so a properly healthy running unit will do the 147 justice if you give it a good service.
1999 156 1.8TS Sport Pack 3
2001 166 3.0 V6 24V Super
2003 156 GTA 3.2 V6 24V
2005 156 1.9 JTDM-Jet Sport
2008 159 1.9 JTDM Lusso
1997 GTV 2.0TS Lusso
2001 147 1.6TS Lusso