groundwire, while i don't really have much personal experience with this level of power, it might be a good idea to take things step by step.
sounds to me like you've tried a lot of stuff, and checked and re-checked things. usually when that does not yield a solution it's because of two things:
1. that thing that seems unchangeable and seems like it just HAS to stay the way it is.
2. that thing that you are SURE it can't be, and by now your brain is passing it over within a second of thinking about it.
Troubleshooting is a universal art and isn't confined to RF, although i've never encountered any other kind of troubleshooting so fraught with anomalies.
first, if you have access to an antenna analyzer that would be a great tool to get some initial data from. maybe see if you can borrow one from someone for a day or two?
how about listing out your equipment chain here?
radio (please list all mods done)- length and type of coax-amplifier (driver?)-length and type of coax- (2nd amp?)- length and type of coax- antenna.
better to start with just the one antenna and get that right before moving on the the directional setup.
set things up so that you are using just the radio, the actual coax that goes to the antenna, and a less than 1 foot jumper placed right at the feedpoint of the antenna.
put an SWR meter in line with that coax, right at the antenna, and read your SWR on channels 1, 20, and 40.
post those numbers here.
if you can't get the SWR below 1.6 here, then stop.
do not add anything else into the equation and fix this issue.
try putting ferrite snap on chokes of the proper mix, (31, 43, etc.) on that 1 foot jumper. like, the whole foot of it.
did that change the SWR?
if yes, you have common mode currents and need to run a good 12" of chokes at the feedpoint of your antenna.
next, does moving the coax around as you are checking the SWR cause the reading to fluctuate? that's a telltale sign of common mode currents.
again, ferrite is your friend.
dont forget to try a different SWR meter to corroborate your readings.
If you are able to get the antenna SWR down to 1.3 or below doing things this way, then add the amp (only the driver if you are using multiple amps) again using the actual coax you intend to be there all the time.
put the SWR meter in between the radio and the amp, using the actual coax that would go to that amp, and again, with a short 1 foot or less jumper at the back of the amp.
check the SWR going in to your amp. what is that SWR?
is it 1.3 or lower?
remember that whatever power gets reflected back to the radio doesn't just stop there, it bounces back and forth down the coax, and will affect the purity of the signal coming out of that amp.
if that SWR is too high, then this is the place to start and you need to make sure that your radio is actually putting out 50 ohms and without a bunch of harmonic content.
that's why i asked about the mods done.
if the radio is ok, then you need to tune the input of your amp to get that reflect down.
if all that is ok, then put the SWR meter back at the feedpoint of your antenna, but this time after the amplifier, again using the actual piece of coax that will be going to the antenna.
did that SWR go up from your initial reading using only the radio?
that most likely means that your antenna has some unwanted reactance or the output tuning of your amp needs adjusting.
the more links in the chain, the more complicated this all becomes but im sure you can see from what i laid out that you need to add things in one at a time to find the source (or sources!) of your problems.
most of us would be fine with an SWR of 1.5 or below, but i understand that at high power levels, you need to be much more critical of your tunings.
please post your results here if you want help determining which piece of equipment is the problem and why.
LC