3K rev limit is guardian mode. I don't have the Verado service manual (I only have an optimax one to hand) here for the list of things that trigger it - but I would expect either a warning to come up on smartcraft, or you need to get it plugged in to a DDT.
I wouldn't run it until you know what the issue is - some of the causes of the 3K limit could cause damage if you keep pushing it - although equally likely it's just a sensor or loose connection. Specifically, if I have guardian mode trigger I'd only run it enough, gently, to get back home safely and not run it again until diagnosed.
Did you buy the boat & engine together from Bembridge Marine (they make the shearwaters?). Jim that runs it has a really good reputation - while he won't be able to plug a DDT (wires are not long enough to reach), if it all came from him I'd give him a call - he's a Mercury dealer too.
And certainly any local mercury dealer will have a DDT - you'll pay a bit for them to plug it in, but since the actual DDT units cost thousands, it's only fair. Unless you are super keen - in which case, I can give you a link to a US place where you can buy your own.