I guess it's time for me to put in my 2¢ worth .....
It's obvious that the Input is not shorted to ground ..... the pictures have proved it. If it had been shorting at that point there would be no output from the amp at all. The only reason for it testing as a short is due to the input transformer's coil wires going to the ground (Class C).
I hope you're not trying to measure a capacitor with a resistance meter....
You say you've watched a lot of BBI's videos, so you must have learned something.
BBI's videos always have shown at least 2 (Bird) meters, one for Average and the other for PEP, noting that Average watts are always lower than PEP. Remember that output power on AM is Average and multiplied by 4 (4:1 ratio) would be the modulated PEP, so you may not be having any problems.
To be further confused, have you read:
* Note that where it states 500w input ..... that's the electrical power to run the amp, not the output from the amp which is 375w
Is the wattage, that you have told us, Average or PEP?
Since you have spent a lot of money that you may never recuperate, there's only one thing that no one has even mentioned .....
Take the entire amp apart to clean up all the flux and terrible solder work. Be sure to take a lot of pictures first and notes. Cleaning and polishing the entire board may eliminate any kind of electrical leakage caused by the mess that could be causing the power loss.
At this time all the same components should be checked against each other to make sure their proper values match ..... including the pills, with a proper test tool for an "hfe" of "62" (62 is the number that matches each pill, one pill could change with time so I've heard.
Before you take it apart, the best way to look at it is that each "2-pill section" and its components have to match the part-per-part values of the other "2-pill section" and its components. The only thing that keeps them working together is the input and output combiner components, a hot or warm output combiner resistor means trouble ..... the output combiner resistor should be as cool to the touch as possible, if hot it would mean a mismatch of components between pill sections.
The easiest way to test for problems would be to feel the temperature of the "output combiner resistor" (while transmitting), if it gets hot you have a component problem.
Apparently, you are doing all your testing in a truck(?), what is the SWR between the amp and the antenna? Have you tried a dummy load, in the truck, instead of the antenna?
Has this amp been tested on a bench with a power supply of at least 14.5 volts and proper amperage supply (you said that your volts drop under load in the truck?)? With the 2-pill amp pushing the 4-pill amp, this thing should be doing a lot more.
Being that it is a class "C" amp, a bias circuit should be added to make it usable on SSB.
Until that board is cleaned you may end up chasing your tail.
73 ..... and may you eventually find happiness with your amp .........