I actually think at this point they may only have circumstantial evidence in the MH case. The DNA they would have run would have come from the shirt they found, and even with a match that only shows contact. We don't know if the DNA is sweat, or semen, or blood... When they announced the connection they specifically said "forensic link" over DNA match which makes me wonder if its something else they found...i have a theory that perhaps when MH purse was found, they were able to recover "fibers" on it...and I think when JMs cab was seized those fibers matched ones found in his cab. Though both of these are strong, and prove her presence in that cab its not enough to prove he abducted or killed her...and I think that's why, as of yet, we have not seen charges.
In the rape case DNA would have to be a match, so presumably it is. If the MH case was linked to the Fairfax case by DNA it could only have been by the DNA of the suspect, so that would imply that they have him dead on that as well. In the HG case they probably don't have a link between him and her, but they should have one between her and him by virtue of her DNA being in the car (it would had to have been there since there would be no other way for him to have been involved).
If the evidence is something other than DNA then it becomes much more murky since there could be alternative explanations for whatever it is. That could be an explanation for why additional charges have not ben made yet. We will just have to wait and see I think.