It is not clear what you have done...What do you mean by
merged the linux partitions back into windows
This is NOT obvious:
even though all of my important docs are on the d: partion and I wont lose them if I rebuild it.
You need to get that data backed up before you do anything else.
Boot from Windows CD--rescue mode, and do "fixmbr"
Boot from a live CD Linux--eg Knoppix--and have a look at the partition tables, booting setup, etc.
If you have no way to get at the data by using something like a live CD, you can always mount the disk in another computer.