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Lahar,
I would recommend using the MASM32 package as its integrity.
The reason behind this, is that that the package is tested by many users for any incompatibilities of the sort you mentioned, before it gets to be released to the public.
If you want to use different binaries, it's ok, as long as they behave _exactly_ as the old ones. Modifying headers in order to get binaries to work, IS NOT A GOOD IDEA.
Imagine that: You just downloaded a cool project that makes use of any of the modified / removed members of the header. What will you get instead of that cool project ?
Answer: HEADACHE & FRUSTRATION !
Also, what happens in the case that you need to use the removed members of the header? Drop the project ?
In conclusion, if the new binaries don't behave exactly like the old ones, avoid using them. Even if they seem to behave the same, just in case, before you actually replace the old ones, save a backup of the original MASM installation folder.
Also, as Japheth pointed out, the ml.exe will not inline/inject .IL to your project, in any case. In addition, i don't think that the MASM binaries have any dependency whatsoever on any version of the DotNet framework.
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