Your thread has got quite subjective... it seems to go in different directions every time I go and comeback... and being 386 related, I like it!
In answer to the thread title though, "the best 386 motherboard"... you have touched on one of my flagship projects. I believe the answer to this would be from the below eight: -

All are 386, and all are VLB. I have tested each to varying degrees, though the project is still very much work in progress. Two things have happened which has slowed things down a little, they are: -
1) Starting a new family (time is now a scare commodity these days)
2) The test hard drive I used went on the blink, along with many of my test results
I will be picking this back up when I get the chance... once the ship has steadied and I sort a new hard drive from the stack.
Regarding EISA, I have done a fair bit of testing on this as well and have made a few threads here on Vogons... some are below in my signature along the bottom of this post, and another is of the various EISA graphics cards that are out there: -
EISA Graphics card benchmark results
There is lots of information and resource to look through/at. It is a fun ride... personally I would recommend you do both a 386 VLB and 386 EISA system, testing them both for yourself and for Vogons, by publishing the results of each online... possibly even comparing them. No better way to learn and support Vogons.