I have been looking at it and finally found the best way to go at it :
Grab IO.SYS and COMMAND.COM from some CABs on the Win ME OEM CD
Those will allow F8 startup menu and full parse of CONFIG.SYS and AUTOEXEC.BAT, full functionality and no patching needed on them !
But there is a problem :
REGENV32.EXE overwrites AUTOEXEC.BAT and CONFIG.SYS files every boot. All restore tools I found patch this program to look for different files instead.
All other tools also use IO.SYS from the boot floppy and that one has only "normal" boot menu option available, the one on CD has all options like 98 and 95 do

I am going to write an automated windows based tool to do this patch business in not so far future.
I am also considering making ME my primary use OS, there's so many improvements to it, especially around networking. I know there's 98SE2ME but I never got it to work on any of my hardware without errors popping up and putting files in wrong places and it seems to be discontinued too.