Yes, the paperwork is misery and it's a process, but one should do it anyway. This gives you a much, much better chance of not having issues like this and if/when issues DO come up, you have a legal agreement in place and a large bank used to dealing with them in a timely manner, with real humans that can fix stuff, if even only temporarily.
Also, you can always go back to doing transactions with Stripe as a backup if need be.