As Paulo alludes to above, it will have to be CE certified in order to be sold legally, unless it is built earlier than June 1998. That includes all systems, including (but not limited to) engine, batteries, though-hulls and so on and so forth. Furthermore a manual MUST exist. A CE certification is a heck of a lot of work, just so You're aware.
There are some exemptions for race boats etc, but I doubt you can get an exemption for your boat.
Paying VAT in Malta sounds like the way to go for that part, but the CE part could well be the more expensive.
Personally I think CE certification sucks, as it also prevents some from building one-offs.
Hope this helps, even though it wasn't the most positive post