One central element that could be used to do this would be to major on the central section of the play, where we see Faustus and Mephistopheles engage in a series of practical jokes which stand in complete contrast to the tragic and momentous beginning and end of the play. To my mind, the central section of the play has always been its Achilees heel in that it is reduced to something of a farce as Faustus shows exactly what he does with such amazing power. Majoring on these scenes and perhaps cutting the first and final act would emphasise the comic element of this play.
I've always found the play -- and Doctor Faustus himself -- much funnier, at least in a darkly humorous kind of way, than it is often assumed to be. Take, for instance, the opening speech, in which Faustus rejects one career option after another, using a good deal of faulty logic in the process. He has studied theology, but he quotes the Bible in a blatantly incorrect way.
Right from the start, then, Faustus can be seen as a somewhat pompous, pretentious man whose pride is fairly laughable. The scenes in which Wagner imitates Faustus further undercut our tendency to take Faustus completely seriously. So does Faustus' later scene with Helen, with her sputtering fireworks.
Finally, in his last speech, Faustus tries to blame everyone and everything but himself for his predicaments -- even including his parents. He continually claims that he "must" be damned, but he never asks God for forgiveness. Faustus can be read as a dark comedy with a definite element of farce.
Based upon the fact that the play depicts a story of one selling their soul to the devil, many changes could be made to add humor to the play. When first in production, the play was outright terrifying to the audience. In order to adapt it to a more comedic form, one could easily characterize Mephistopheles in a more comedic light. In Act I, scene iv, when the devil appears, Faustus' evoking of the "spirits" could be over-dramatic. This over-dramatization of the evoking and appearance of the Devil, if done with humor, would set the mood for the remainder of the play. (Think the use of the witches in Shakespeare's Macbeth in the opening act. The mood, dark and ominous, is set from the very beginning.) Instead of opening with the determined mood, the showing of the "comedic" incantations (the use of gibberish would add effect) and the appearance of the devil (perhaps showing his confusion at being summoned) would prove the play to be seen in a more comedic light.
Then, it would be a tragicomedy. According to Philip Sydney tragicomedy was a "bastardly genre" and he castigated "the mingling of kings and clowns", calling it "a mongrel tragicomedy." In this respect, the comic scenes in The Tragedy of Doctor Faustus most certainly present affinities with a tragicomedy. Yet, I can't see how you can possibly cut the final act. Perhaps instead of cutting it, one could resort to a deus ex machina, as in Shakespeare's problem plays or tragicomedies, and suggest Faustus was saved at the last minute. One of the main differences between jealous Leontes and Othello is simply that one is saved, is given a chance to repent and make amends and the other can't be redeemed and meets his death at the end of the play. Faustus was not damned because he committed murder so, I can envisage a different ending. If the ending is to be a moral one, then the end of the Winter's Tale or The Merchant of Venice can possibly serve as models: a human being assuming the function of a god as a deus ex machina!