I would set him free, because I realize it would be my duty to do so. If I can't say they've convinced me beyond a reasonable doubt, it doesn't matter if I suspect he did it. It's my job to keep the prosecution to their burden.
The doubt for me is that there are too many assumptions we have to make in order to make the prosecution puzzle stay in place. We have to assume he stopped for gas, possibly more than once. We have to assume that he manipulated the cameras. We have to assume that he was able to evade all the other cameras in the HI to not be seen, and that the gas stations that he stopped at had no cameras. We have to assume that he was wearing the HP shoes in Cracker Barrel. We have to assume that he was lucky enough not to transfer fibers, blood, or bodily fluid, even though he didn't clean up in the house. We have to assume he made it back without speeding, without getting stopped by police, without getting recognized by anyone who knew him or would positively ID him, snuck into the hotel, then made it to his appointment without anything going wrong (meanwhile disposing of evidence). We are told he either acted in concert with another person, or alone, but we have no evidence on that matter. We have to assume that he didn't have any scratches on him because he was wearing gloves, but he left a fingerprint on the wall because he wasn't. We have to assume both FH and CB were wrong about their IDs.
To me, that's a whole lot of assuming.
ETA: Sorry if this is rambling or confusing, I wanted to respond to your post right away, and didn't put a ton of thought into everything I might have left out.