OK. Not sure of the how or why, but after some reading in the good old MS knowledge base I extracted wininit.exe from my win98 cd since wininit.exe was missing from my windows directory for some reason.
So it boots into windows now which is great, but I am still very bothered because I don't know why this happened...and because it took me about 8 hours (on and off) to get the dumb thing going again.
Does anyone have any suggestions as to why this stuff happened?
By stuff I mean the missing emm386.exe, missing himem.sys, missing wininit.exe.
For now