The part numbers are not intelligent(outside of ManEx they have no meaning).  Without the software to provide complete information, it is just a number.  The main concern when creating a part number is not to ensure a sequential part numbering by class, but rather the ability to track additional information (AVL, on hand qty, where used, standard cost, etc) by one internal part number.  Because of this, the actual number doesn't really matter as long as the system knows which additional information to attach to the internal part number.  This is why ManEx works as well with a manually created number as with an auto-generated number.  If you use auto-numbering, the numbers can be arranged on the shelf in ascending order (even if there are gaps between the numbers).  The auto-numbering in ManEx simplifies the part number creation process and provides a count of the total parts in your system (141-0001000 to the 1000th part loaded).

Additionally, it is common in this industry to add new parts and obsolete old parts as the customer base changes and grows over time.  Even if the parts were setup sequentially by class and type, as you suggetsed, they would eventually have gaps in the numbers as old parts are made obsolete.  There is a no way to prevent this and it is not worth your time to fix it after it has occurred.

Not having all parts numbered sequentially by class and type does not affect the quality of the information provided.  Users are able to purchase, track inventory, and kit all parts by part number.  ManEx will still accurately maintain all important information by part, by customer, and by BoM.

If is absolutely critical to have all parts by class and type sequentially numbered. Users do have the option of manually creating the part numbers.  This will allow you to use any part numbering method. 

Go to the Number System module to Setup "Auto" or "Manual" numbering.

Note:  With the auto-numbering setup the way it is you can have 10 million parts in your system.