One big change since '99 is the higher floors. Both because of taller frames (with the 24 and 26k GVWRs) and the raised sub-floors to allow full size baggage compartments below the slides. This means the doghouses are smaller, and there is more room for insulation.
I test drove a Canyon Star 3920 (the toy hauler), and engine noise was very non-intrusive. The normal coach noises were far more annoying.
The 7.3L gas motor is quite a bit shorter than the V10, so once they are in full production, the coach builders should be able to build nearly flat engine covers. Seems like the first ones one are still using the V10 covers. Ford included. Current 7.3L E450 uses the V10 engine cover, but they say a smaller cover is coming out in January.
2000 Ford E450 V10 VAN! 450,000+ miles
2014 ORV really big trailer
2015 Ford Focus ST