Jezter!*+$nothername's Journal: Never ignore a "Windows will now restart" message!

I have encountered a major, major, problem with a production machine. I admit that is was of my own making and I blame no-one else.
The story so far: I have one machine that was running Windows XP SP1, it just happened to be my main production machine. It wasn't SP1 out of choice, I wanted to patch it to SP2 but each time an attempt was made I got an unusual error message (just before the SP2 update failed) saying that Windows could not read or write to the database. This perplexed me no little mainly because, to my knowledge, there was no database present on the machine and secondly, even if there were a database present, why was Windows trying to read it anyway? Some digging around produced an element of explanation: for "database" read "file system"! So, Windows couldn't read or write to its own file system? It managed every other patch and update, what is so special about SP2?
The machine is quite large and carries two hard drives so, my obvious move was to put Acronis Disk Director Suite on the machine, do some nifty partitioning and copy the "C" drive to a back-up. No problemo. I then force fed the machine a repair console job from the original XP disk to rebuild the system into something that Windows could read and write to. So far, so good.
I then applied all fixes and inserted the SP2 disk. Yay, it worked.
Then I looked at the partition tables .... I'd acquired 2 new partitions? One claimed to be empty (just under 1Mb), the other was about the size of the original "C" partition. I rebooted the machine. It didn't like it! It was cross booting from two partitions. The boot.ini file was on one partition and the system files (particularly NTLDR) on another! A search produced the unexpected result that the boot.ini file was on partition "E" and NTLDR on "C". The obvious solution seemed to be to make a new boot file and place it on "C" ... ok, I know now!
I'd just finished doing something else and was returning to the boot.ini problem when a bit of maintenance software, that had been running in the background, popped up a message to say it had finished doing its job and would now restart Windows, was this ok and if not click "Cancel". I wasn't quite on the ball as I ignored the message. The machine shut down. It restarted and ....
Acronis cannot find NTLDR "Press etc., etc., to restart". Switch boot discs and Windows cannot find a valid boot.ini, "Press etc., etc., to reboot". There's an empty boot.ini file that doesn't tell either method of starting where the "real" boot files are.
Having spent nearly two weeks on this I'm about to have a go with fixntldr (from the incredibly helpful site http://tinyempire.com).
Have I tried the Acronis rescue disk (yup, I made one)? Yes, I can even see the empty friggin' boot.ini file but when I try and delete it, the system crashes and when I reboot the rescue disk the sodding file's still there! The Windows install disc? Yup, it tells me that it cannot find a Windows o/s (not so suprising as it's hitting the Acronis o/s selector and not getting any further). A reinstall also fails as it's an XP upgrade disc and is looking for an older o/s to update from (long since deleted) and all I have is an OEM recovery disc.
I hope to be able to get into one drive at least, recover what I can then attempt to rebuild the o/s.
All because I created a system file and delayed putting any information in it and then ignored a message that I'd ignored on a regular basis for several years - never again!