I've never done a Friedel-Crafts reaction before... seems like it's on of those reactions you should do at least once.
Is it possible that your product is just a very viscous oil and you have some slight impurity in there adding the black color to it? If that's the case, I would try using some charcoal to filter out the colored impurities, I've done it before and it seemed to work fairly well (and it's been suggested on the forums a lot before, too I believe), just be careful not to lose your stuff on it. It is an acid, however; I think if you ran a short column, you could probably get it off the silica without losing any. What does the TLC look like? Just a big spot at the bottom, or is it a mix? I've performed column chromatography a few times on some acids and it seems to work out alright, you can sometimes spike the solvent with a little acetic acid to help prevent streaking down the column. Or maybe just a quick acid base extraction could also get rid of the impurities too, I do that when I'm feeling particularly lazy or my reaction is about spot to spot.