Hmmm that's a lot of touch points to hit, I doubt one single service or software can manage it all, and you'll have to either make some consessions or you'll have to play the middle man between all the software in play

I have worked with 1 non-profit and while they wanted to accept Bitcoin, they didnt' actually care too much about it, it was just an add on and they are more focused ont he cash and there isn't anyone technical to manage it so they went with - https://thegivingblock.com/ and for LN they're using a local payment provider that is linked up to moneybadger but on their end all they get is cash

For the front end its going to depend on how involved you want to be you can use something like BTCpay or Zaprite https://zaprite.com/ - if you're running a node yourself or something like https://paywithflash.com/flash-automated-treasury-early-access/ that you can hook up to a node or albyhub for example

As for the holding of funds, you'll need a few technical people onboard to each manage their key which is a ball ache if you do it DIY

Or you can look at something like unchained

https://www.unchained.com/donor-advised-funds

Who can at least come in an advice

but for every company you bring into the stack theirs costs involved! More DIY is cheaper but a lot of time involved in upkeep