dbur,
Yes - the mapping tool is not ideal for very large parts (connectors, FPGAs, etc...) also the default 1:1 symbol to pin mapping was taken out in v11 for unknown reasons so its currently tedious for large parts. There is an active request to get this updated within the tool but the exact timeline is unknown. However, I may have something to help you that I did in v10, but it needs some updating for v11.
Please send me an email and I will give you the details. Also I want to get an update on how your other issues are being addressed.
Regards,
Pat Noonan
National Instruments
patrick.noonan@ni.com