So you're saying you just updated to 2.1.0-4 and just copied the 1.43 firmware files into the R4 3DS SDHC and it worked without doing anything else? I don't want to update because I don't have a second DS to flash the flashcart in case it stops working and it's really difficult indeed to find...
Legit.exe is the only way, or the most reliable as far as I know.
I think the link in the downloads section is not working but there's a link inside their forums (I'm not sure if I can link that here or not)