He is able to boot into recovery console with no problem.
Oh, I thought he was having problems booting into RC. At four or five pages, I start getting confused, I suppose!
OK, I just re-read the thread. It looks like OP can boot into RC after all. It's just that when he chooses to boot into regular Windows XP (on the hard drive), he has problems.
OP: Did you ever successfully run chkdsk /r after booting off the CD? I re-read the thread, and I'm not sure you did that.
If the problem turns out to be malware-related, I think a Clean Install is probably indicated at this point.
OK... Just saw this nugget again:
ok did that but now im getting another new error, I get to select window to run but then get this message:
Windows could not start because the following file is missing or corrupt
\minint\system32\config\system
You can attempt to repair this file by starting Windows Setup using the original Setup CD-ROM.
Select 'r' at the first screen to start repair
I went into the repair option but could not find how to fix this, I have just run a chkdsk /r but I am still getting the same file.
I think when you attempted to rebuild your boot.ini file, there was some leftover stuff and you are now being given a choice of Windows installations to boot off of. (This is why I had earlier relayed Jose's instructions to rename the old boot.ini file.
The "minint" reference might be a clue.
When you boot off your hard drive, describe in detail everything you see on the screen. So far, all you have told us is "I get to select window to run," but I am unclear as to what you mean by that.