A little confusing on how the OP has things all wired up but I can say an AGC amplifier can be troublesome. They work great on a test bench but hooked to an antenna, signals from the police car down the street or fire truck up the street or the ham operator two doors down will cause the gain of the amp to run all over the place and can affect what makes it to your TV receiver.
It sounds like you might be pointing two different antennas in the same band two different directions then combining them. If you have a preamp on each antenna before the combining process it should be ok, but if your using a passive combiner (splitter) and a preamp after the splitter you will loss more than half the signal off each antenna in combining. If you combine two identical antennas pointed at the same tower and at the right spacing you can get up to 3dB gain, but pointed different directions you lose 3dB or more. A combiner for separate VHF and UHF antennas has very minimal loss.
If you have preamps up at the antennas your coax loss will be less of a concern, but I would use a good quality RG-6 at minimum and I don't use RG-59 for even short jumpers any more. If its a really long run and most of your reception is UHF then RG-11 is nice.
It sounds like you might be pointing two different antennas in the same band two different directions then combining them. If you have a preamp on each antenna before the combining process it should be ok, but if your using a passive combiner (splitter) and a preamp after the splitter you will loss more than half the signal off each antenna in combining. If you combine two identical antennas pointed at the same tower and at the right spacing you can get up to 3dB gain, but pointed different directions you lose 3dB or more. A combiner for separate VHF and UHF antennas has very minimal loss.
If you have preamps up at the antennas your coax loss will be less of a concern, but I would use a good quality RG-6 at minimum and I don't use RG-59 for even short jumpers any more. If its a really long run and most of your reception is UHF then RG-11 is nice.