One other question if you dont mind, how do you tie your naming system in with your suppliers so that everything gets ordered correctly.

That's why I suggested to talk with your buyers and suppliers.

Mike - Not sure what you have looked at so far, but the best practice for 'common' parts would be for them to be descriptive in nature. Example: Bearing, Roller, Sealed, 2 in ID, 2.5 in OD, etc... The method here is to assign a Class and Subclass to the part and then any specs that you decide should be included. The other parts you will have are refered to as OEM parts. Parts that are specific only to a particular piece of equipment. These would list the specific equipment that they go to. Example: Filter, OEM, for Tertiary Screens.
I do not know which CMMS you are implementing but you can insure correct ordering of parts through your vendors by including their part number in the Inventory module. Most software will have a place available for this information as well as a manufacturers part number (sometimes the same as the vendor's). If yours does not, remember that all the screens can be customized to include any information you would want to see. Use of these part numbers in your system as a secondary reference within your storeroom will solve your problem.
We have scrubbed and normalized numerous inventory databases for many CMMS systems and these methods always bring the desired results.

We will be going with JD Edwards at the end of the year. I am not real excited about JDE maintenance module but thats what I get to work with.

The CMMS selection is what it is.
I hope for your sake that it is not just an "IT or Accounting Project" for your company but rather one that is integrated with all end users in mind and the time is being taken to insure that the correct information will exist in the correct format.
Remember, your CMMS will store a ton of data for you but if it is not set up correctly for you to be able to get that information back out, what good is it?