First a little explanation of what we've done, then some thoughts on what happened and what we can try to fix the boot problem.
ComboFix does many things: First it very specifically targets certain malware and puts those files it identifies in quarantine. It did this with the files listed in the "Other Deletions" section of the log you posted.
It also lists files recently created with the idea that it cannot have signatures for every new variant of the malware it targets. This list must be manually analyzed which is what led me to have you delete trusted.exe.
Another function is a rootkit check which led to deletion of srosa.sys and hidr.exe (I should have included another file in this list of deletions but neglected to include it in the list - we would have picked this up with the second ComboFix run). The two we deleted here also appear at the very end of the BlackLight log.
All of the things we deleted are related to a rootkitted version of a bagle trojan that was responsible for killing avast! (rootkit is a term for a program that hides another program), a couple of backdoor trojans, and some spyware.
With one exception the lines we fixed in HijackThis were all registry entries referring to files that were were already gone. I did this for tidiness - to make it easier to review subsequent logs and just to make things run better. The single exception was this line
O4 - HKLM\..\Run: [ratmn] C:\WINDOWS\ratmn.exe
Removing this line by "fixing" it simply prevents ratmn.exe from loading when your computer starts. We did not delete the file yet. I have not been able to identify this file which in itself makes it suspicious. It is most definitely not
a Windows system file and, since you cannot find it when looking manually, appears to be one of the files the remaining rootkit may be hiding. I would still like to scan it at Virus Total before deletion.
I think the boot problem is caused by something, probably malware, corrupting your operating system. This can be seen in the very first lines of the ComboFix log
C:\WINDOWS\system32\chkdsk.exe not present
ADS removed - C:\WINDOWS\system32\ntoskrnl.exe: The system cannot find the file specified.
Although the computer can boot without chkdsk.exe it cannot boot without ntoskrnl.exe. ComboFix did not remove these files - it reported their absence. I am somewhat surprised the computer made it though the previous boot.
In order to fix this we need to replace ntoskrnl.exe and I think we may be able to use any XP installation disk to accomplish this. Is your
computer XP, and do you have the Windows disk for it?