Did you try to start the console without the SD card? Sometimes after a downgrade on N3DS the console give a black screen on the first boot when the SD card is in.
For the MD5 you should use the same software they used to generate the MD5. All MD5 generators don't use the same algorithm so you could have different results. If the MD5 still don't match download the files again.
It also helps to directly extract the updates folder on the SD card instead of extract it to PC and then copy the folder to the SD card.
I never succeed to downgrade with safesysupdater but it should work fine. You should at least use it to check the files.
For the MD5 you should use the same software they used to generate the MD5. All MD5 generators don't use the same algorithm so you could have different results. If the MD5 still don't match download the files again.
It also helps to directly extract the updates folder on the SD card instead of extract it to PC and then copy the folder to the SD card.
I never succeed to downgrade with safesysupdater but it should work fine. You should at least use it to check the files.