Does it seem as if you both are able to work together to help find a more practical financial solution? If needed?
^ If yes, Then the ECM is an pretty easy bolt on part with 3 bolts 2 plugs that you ought to be able to do yourself at home?
Maybe pay what's owed to the service guy, bring boat home, remove ECM, call and mail it in, have them check the ECM for $100 and if needed and possible as they should be able to tell you what failed and try to ask them what seems to be the general cause of that particular failure in hopes to try and maybe solve a still possible unseen potential issue so it won't continue...Have them fix it for $650.00 and go form there...That or you call for a price and order timeframe and have the service guy install it if he's willing vs him buying new at 2k,
http://mefiburn.com/mercecms.asp
With the continual possible issues I mentioned above, I'll just mention generally it's considered a better idea to try a thought to be bad ECM out on a known good running engine "first" 'That way should there be a bad wire/component, etc. on a none running engine it won't harm someone else high $ ECM.

...With that said, it seems as if maybe your engine is going to be good/okay as it ran your engine already and didn't hurt the other ECM.
Just some ideas for you is all.