Although all the pre-2009 FX HOs are essentially the same machine, Yamaha did make subtle changes (especially with the 08). I suspect that in your case the 06 engine would work just fine with the 05 electronics. You might want to include the 06 wiring harness in the move then if you had to you could swap the ECU and display.
2008 Yamaha FX HO Cruiser
2010 Hurricane Sundeck 2100