Haha, so many questions.
We had a company shuttle our suitcases to hotels for us as this was DW's first time cycling as an adult.
The trip was a success and She is keen to ride unsupported next, and to take on a bigger challenge. Meeting others on the road carrying camping gear etc helped to show what was possible.
DW was basically scared of bikes prior to doing this. It was a big deal that she agreed to do this.
We did very little preparation. We borrowed a bike for DW about a month ahead of going, and we rode together maybe twice a week for that month, building up to 50km rides.
Due to the lack of prep, the first few days were tiring and our legs were sore, but we got cycle fit pretty quick and by the end of the two weeks our legs were good.
We had no rest days. Just rode 12 days straight from Passau to Budapest. I'd recommend to anyone else doing it to have a rest day in Vienna mid ride, although it was ok without one as day 8 was only 20kms so was basically a rest day (day 9 was 85kms our longest day). Anyhow, having only half a day in Vienna didn't allow for much sight seeing so an extra day there would have been good.
The section from Passau to Vienna is perfect for non-cyclists as it is pretty much dead flat (unless you do some side trips like we did into the surrounding hills) and there are restaurants every few kms to act as a distraction.
The scenery is also probably more spectacular over this section, but the downside is that you will see hundreds of cyclists every day. Most cyclists are over 60s retirees. Many are families. This didn't detract from our enjoyment, but undoubtedly will be a big turn off to some. I have heard that in August it's pretty painful with so many kids on the route.
From Vienna onward we saw only a handful of cyclists each day, and a lot of the riding was through farming areas without the glorious views of quaint riverside villages we had on the first part. But the pay-off on the section from Vienna to Budapest was that the towns and cities we stopped at each night were more interesting places than the first part of the trip (eg: Bratislava, Gyor, Visegrad). The last 2 days into Budapest were really nice rides.
In the end, I'd recommend both halves of the ride. The whole trip is a great, safe, easy introduction to cycle touring. The distances were 50-60kms each day. We ended up riding a little over 600kms over the 12 days.