Complications caused by FPForce's highly customized Non-Profit Success Pack upgrade/conversion to Lightning Experience

I'm a new administrator at my nonprofit, and my first overeager act was to convert our whole system to Lightning Experience.  We run a customized version of NPSP for our specific program, and the only thing working cleanly before I rolled out my initiative was the converted Opportunity to Donation. When I updated NPSP, I was made to add "Prospecting" to the picklist for Donation Stages.  Now, that is the only Stage I have access to.  If I enter a payment while entering the Donation, the Donation stays at "Prospecting", despite being paid.  I've found a multi-step solution that involved setting a trigger to switch the Status to Closed Won when I enter a payment separately, but this means first I must create the Donation (Opportunity), save that, add a payment in a different tab, save that, then never touch the Donation again, because if I open it, I don't have access to "Closed Won" and I'll save it as Prospecting again.

The options are all available in the picklist.  If I try to Delete or Deactivate Prospecting, I get an error message saying that I must add more options to the picklist for Grants and Donations because it is the last option left. I've hit a wall, there's nothing to edit to make this work.  I've tried creating new options, activating old ones, deactivating old options, deleting and recreating them, and still haven't found a solution.

P.S.- Possibly related, when adding a donation from a contact, I get a new window that starts the process in Object Manager. Not certain what that's about.

P.P.S- Also possibly related, I added a new option to our deeply customized picklist for "Case Management" and It refuses to show, despite active.

P.P.P.S.- Also also possibly related, the Dashboard can't be changed, and the graph of donations shows "Add the donations you're working on, then come back here to view your performance."

Help me Obi-Wans. And @Emily Parker