this depends on whether C, D, E are on one hard disk or more than two disks. it should not be hard. you can try do it in 98 which is on C because computer check C first automatically when booting up.
here are lots of info from google.
http://www.google.com/search?client=firefox-a&rls=org.mozilla%3Aen-US%3Aofficial_s&hl=en&q=edit+boot.ini&btnG=Google+Search
another way is to use bootmagic. bootmagic cann't be in NTFS so install it within 98 then it's very easy to control all boot options. bootmagic 8 has GUI. good luck
i don't think you need to reinstall xp on E. since you followed instructions, then you probably didn't install xp OVER 2000. this means, D partition might just be inactive at this time. you just need to heve computer find D partition