Howl is about madness: it's supposed to be confusing. That's the point. Also, Ginsberg never thought it would be so widely read (source), so it contains a lot of references to people and places that his friends would have known about, but which require a bit of explanation for the contemporary reader. (e.g., "N.C." in line 43.) On the other hand, the use of the "long line" that Ginsberg borrowed from Walt Whitman gives the poem a rhythm that resembles ordinary speech. Try to keep up with the frenetic speaker and his intense emotions, and don't worry too much about making sense of every last word and detail.