We used the link provided in the Getting Started guide at NMLS:
Go Here To Acquire then chose the free toolbar download.
You will have to pay the $55 per admin directly to the Registry when you establish the admin accounts, same with the $100 for registering the bank, and the fees for the MLO - which will include the NMLS registration fee AND the fee for the background check and fingerprints.
The Registry has been very responsive. We've gotten as far as signing up the admins and tomorrow will submit the MU1R for the bank. The only reason we're waiting until tomorrow is that we are a small bank and the other admin and I are busy with month end reporting this week.