I'm not surprised that you're having issues with selected channels with the two-antenna setup. The sensitivity of the HBU is not zero off the back, so you are getting Richmond signals in both antennas. If the signals don't arrive at the same time at the combiner, then destructive interference happens and you end up with
less signal than you would have with just one antenna. Ideally, if you had an antenna that was equally sensitive in two directions ("front"/"back"), then that would be the best solution.
You mentioned a home made antenna. What type? Yagi? dipole? bow-tie? Since you are not adverse to building from scratch, I'd recommend a 4-bay bow-tie array with no reflector. See
here for plans. If you built the "Youtube" bowtie array with 5 1/4" spacing, then that is a far less effective antenna.