Updating Stock Rom with .NET 3.5

[santino405]

Im building a rom off the stock rom base, and i would like to remove the stock .net and replace it with .net 3.5. I've been reading up, and i've gathered that if you install 3.5 over 2.0 some apps will not be take advtange of having .net 3.5. I've tried replacing the NETCF folder in the sys folder with the NETCF folder for 3.5 but this caused alot of instabilty, I've built an OEM from the NETCF cab. but i have a feeling that using the oem will not completely uninstall the stock .net. If any one could be of help pointing me in the right direction it would be greatly apericated.