So I downloaded the DSi data transfer to 3DS app and right after it downloaded my DSi shut off. I turned it back on and I got a black screen and it said to turn of my DSi and look at the troubleshooting manual. It now shows that screen whenever I turn it on and I can't get passed it.
... Whoa, that sounds like something serious. I unfortunately have no experience with the 3DS, and thus no advice, but you might want to contact Nintendo themselves over such a fatal programming error. I doubt that's something you could fix on advice alone, sorry to say.