What you should do is identify modules that use transparencies and add some IF statements to make it compatible for example:

This is from Ghost:

If notransparencyfade = 0
If WinXP = 1 OR Win2000 = 1
EnableTrans "1"
Else
EnableTrans "0"
EndIf
Else
EnableTrans "0"
EndIf

This set the vars to either use transparencies or not

This is from Freedom

IF Win2000 OR WinXP = true
*NetLoadModule grdtransparent-1.1_beta_1
ENDIF

This is a bit simpler but does the same trick

If you figure out why they have issues with 98 you can fix it simply by useing these statements.

My suggestion would be to examine theme.rc files for IF WinXP or IF Win98 staements and make a text file to store them that way you can replace the offending with more polictically correct statements or just delete it.