The black screen, I guess is caused by the .. guessed it already .. card reader. I wouldn't worry too much about it, if the dumps are identical and of proper size (mentioned in the 3ds hacking FAQ).
I've been getting many different error codes with that cheap generic reader I mentioned in previous post, also black screen boots and normal uninterrupted boots (to 3ds main menu, like no card reader present at all). Unreliable it is, but seems to read fine if you just get it to brick and not booting to main menu.
All dumps seemed to be identical, before that uninterrupted boot ruined the consistency by writing into nand.
E: Pictures of my completed mod. Apologize for really bad camera, but this is all I have right now.
So I ended up using standard 5-pin electical terminal block as a connector after getting real tired of the micro usb crap, I don't know if the female pins I had were defective in some way but they got broken almost by looking at them in a mean way, when slightly bending wires etc (yes, the actual solder pads on the usb itself broke off from two of the connectors, rather than my solder joints, total crap). Could have used a 4-pin alternative but I had these on hand and thought it would be nice to leave one unused for any potential needs in future, like the usb also has 5.
This one goes to the "blatantly obvious it's a modded console" league but I don't see anything wrong with it. It doesn't require the removal of back plate to get access to it, nor is there chance for user error by plugging charger into that slot, a potential problem with the usb mentioned earlier in the thread.
I used a really small hand file to do the hole in the upper housing, took about an hour to finish. The connector fits there really nice and tight, with a little help from a drop of epoxy glue. I also have a dremel tool, but found this one better to be done by hand, if you just have the patience.
Unfortunately I don't have any pictures of the unfinished work.
The finished side of the 3DS, notice the black connector:
No visible changes to the upper size of the upper housing:
Type of connector used, super-sized view: