I have a new 3W-100, and I mounted mine with 1/4-20 socket head bolts (2 1/4" long). You are right in that they don't fit that well, but if you push them through, they will go. You may have to twist them in, and it will scratch the finish a little, but they should eventually fit.
As far as throttle is concerned, I made an aluminum arm that offsets the pivot using a ball link. I normally make arms like this for all my 3-w motors
I'm enclosing a picture of my installation from my web site, there are also more pictures if you click on to my site.

http://www.samsrc.com/Extracontruct3.htm

Hope this helps

Sam