@Bryant we have spent into the hundreds of thousands of dollars (not including the maintenance and software) and more than 4 years in getting our Windchill system to work the way we wanted. At first we tried just having CAD admins do it with help from IT, but as you are finding, it is not possible. We quickly found that there is no one at PTC who understands how it works holistically. They can offer support on specific details, but we found we didn't even know what questions to ask.
Everything requires customization from simply getting correct mass data out of Creo (yes, at this tme it still doesn't do this out of the box) to exporting useable bills of materials. You essentially get a framework and options that do things that companies might need, in a terrible interface, and you have to customize it to do something useful for your company.
We tried hiring consultants to configure it, but that only got us part way. Finally, we ended up hiring a seasoned Windchill administrator, who previously worked at a well known Windchill integration company. That's when all of the pieces finally fell into place.
Now we have a fairly robust production system and a stage system to try out upgrades.
The initial quote we got from PTC to upgrade from Intralink to Windchill was $50K; in reality it is an order of magnitude higher and you'll need to hire at least 1 person dedicated to getting it configured and keeping it running and nothing else. You'll also need other people who can support java, system building, network monitoring, etc. And you need the entire company to be dedicated to using it and working out the bugs. It also requires that your processes are well defined and you have a clear plan on how you want to use it.
I would say that customers who want to undertake a move to Windchill should expect to spend half a million dollars, minimum, for a small enterprise.
If you need help, PTC will only lead you to frustration. Instead, contact the following companies who helped us immensely:
Fishbowl Solutions
http://www.fishbowlsolutions.com/index.htm
Datafrond