This was certainly a lot more work than I would have ever anticipated with the IDD.
I used a combination of IDD fixes and surface removals and replaced them with native Creo features.
Don't ask me how I got the things to work in the IDD because I honestly do not know. Removing the 2 fillets (rounds) and trimming the surfaces together were done in IDD. Fixing the one corner somehow got fixed with IDD.
I had to fix a sliver in the 3rd fillet with a boundary blend. And I had to create the edges with individual boundary blends. Subsequent merge features finally closed the entire volume to allow the solidify to work.
I used the technique I described above for creating axes for the hole features.
I have attached the file in Creo 2.0 full version and a STEP file. In some cases, I would even opt to use a step version in my Creo session just to "lock" the file from failing in the future.