First, please see my comment to the question. Don't you think you underestimate the complexity of this problem? It's just hardly possible to give you any definitive advice in our Quick Questions & Answers forum, however… well, keep reading.
I would be interested in development of a brand new OS based on CLR very much. Event though I have some considerable experience in system programming in the past, I would not dare to start such project right now, but if I did, I would first start fully on my own, pretty much as you did.
But after some successes and some failures which would help me to understand the problems much better, I would still look at existing projects to learn how they work.
Here the ones I would look at thoroughly:
Microsoft Singularity:
http://en.wikipedia.org/wiki/Singularity_%28operating_system%29[
^],
http://research.microsoft.com/en-us/projects/singularity/[
^];
Cosmos:
http://en.wikipedia.org/wiki/Cosmos_%28operating_system%29[
^],
http://cosmos.codeplex.com/[
^];
SharpOS:
http://en.wikipedia.org/wiki/SharpOS_%28operating_system%29[
^],
http://www.sharpos.org/[
^];
I also understand it you don't want to participate in any of those projects, but I would still think about it.
There are other developments which would not provide source code for you, but it would be just good to know they exist:
ETH Zurich — Microsoft Research Barrelfish:
http://en.wikipedia.org/wiki/Barrelfish[
^],
http://www.barrelfish.org/[
^].
Microsoft Midori (code name):
http://en.wikipedia.org/wiki/Midori_%28operating_system%29[
^].
It would be really great if you could advance this work considerably and report about your progress. I would be happy to read about it in CodeProject or from any other source. If I like the work, I would consider joining it. :-)
Good luck,
—SA