You need to give some serious thought to how you are approaching this problem. There may be commercial products out there that meet your needs, but there isn't anything freely available that comes even close. I haven't seen any clear reviews of commercial tools in this regard.
The Linq2Sql O/R Designer doesn't scale, as you've unfortunately found out the hard way. Something like SQLMetal will scale much better, but it's not a perfect solution either.
Unfortunately, it can be very painful to switch from using the O/R Designer to SQLMetal as they don't share as much code underneath the covers as you would hope.
If you are trying to use a large database with Linq2Sql, you almost have to find and adopt a commercial tool of some sort. One free option worth considering is Damien Guard's LinqToSql T4 Templates, but it's not even close to a WYSIWYG tool.
Switching to a more capable ORM is also going to be difficult.
I wrote a blog entry on this subject some time ago and I've rehashed a lot of this already in this answer:
Do not use the Visual Studio 2008 LinqToSql O/R Designer
Good luck.