While I understand your concern, much of what you've posted doesn't quite hold true. I'm using an older system from well before the Patriot Act and the spying/intrusiveness that has followed it. I trust nothing newer from Windows. The measures I've taken to defend key components of it are extreme even by paranoid standards.
click start, click programs, click accessories, click notepad, open any dll file any one of em or open any executable (.exe) .....If you can read anything in these files they have been rewritten, on the fly as its installed
I can read some of any DLL or EXE that I open in notepad. This is normal. Not the whole files, but part of them.
Apparently you're concerned about your BIOS being compromised. Regardless of how this would be accomplished, it has to be done by a running process. Does your system include HIPS (host intrusion prevention system) and process monitoring/control? These don't use signatures and will detect this kind of process. Concerned about CIA or NSA backdoors in such software? The best software of this kind comes from Russia, and I highly doubt they'd allow such a thing to be inserted. If you think the BIOS is already compromised, reflash it. Just make sure you use the right one or you may kill it yourself. I keep 2 copies of mine, which was obtained before all this ever started.
There are many things you can do to make sure you aren't compromised, especially with the older systems. DOS can be your best ally here. With it, you can protect system files, program executables and DLLs, even the entire registry. On a Win98 or WinME, here's how you do it. Modify it to suit your needs. Just don't use this on any newer operating system than WinME. http://www.freewebs.com/herbalists/index.htm
Worried about back doors or deliberate vulnerabilities in the software you use? The answer is 2 words. Open Source.
I do understand what you're saying here. This is becoming a frightening world. I wholly expect to see WW3 in the near future. As for deliberately compromising peoples PCs, phones, etc, yes, it is happening. To what degree, who knows. There isn't that much of a need for them to do so when they have free access to all communication and internet traffic. There's not much we're going to do to stop it, but I would make a suggestion. Don't make the problem bigger than it is. The vast majority of PCs are already compromised, some estimates claiming over 90% of them. It doesn't take the CIA or NSA to do this. Look what's been done with trojans and rootkits to date. Just because a file can be partially read doesn't make it compromised. You'll end up worrying about problems you don't have, like compromised files that aren't.