You know, before we bought our 2005 400 trawler, I was worried about the poor reputation for quality that Mainship has but we just felt that boat checked more of our boxes than anything else we looked at that was even close to our price range.
I realize you are not looking at our exact boat, but I can tell you that I have been pretty pleased with the build quality of our boat. It is not perfect (perhaps you have stumbled upon my post about the crazy wiring for the fwd cabin lights) but I really haven't found anything major. We have had the boat two years now, and have put about 400 hours on it.
Just from looking around at a lot of Mainships, it seems to me that they improved their overall quality about 2003 or 2004. I don't mean to dis anyone's boat, but the 400 has a lot of things that I much prefer from a build and design standpoint to the older 340/390 which went out of production around 2003.
For us, a big thing was that they use quality components for the most part. A Vacuflush head is a Vacuflush head wether it is in a Mainship or a Nordhaven.
We looked at the Back Cove a little as well, I just couldn't do without a flybridge and the $ were quite a bit more.
One advantage of buying a used Mainship is that there are a lot of them around, so you can play one off of the other to your negotiating advantage. That is what we did and bought our boat about 15% below the market.
Sorry to ramble, and I hope this helps.
Doug