TS-2000 ATU will only tune on 50MHz band, even on a dummy load reports "SWR" in CW on all lower frequencies. With the ATU switched out, the internal SWR meter reads OK.
Set the radio to 1.8MHz, FM, 10W. Connect a dummy load and transmit. Check the RF waveform from the PA board (use a scope to probe the 2 output transistors).
If you do not see a sine wave then there is a fault on the output transistors or (more likely) the two driver transistors. You should see sine waves on the collector of each transistor - anything else shows a fault.
It seems like the harmonics in the odd waveform get through the bandpass filters and confuse the ATU's phase/magnitude measuring circuit.
If the driver transistors have been replaced, check the resistance from their bases to ground. If the resistance is less than about 45 ohms then the green surface mount capacitor from the base to ground has probably been touched with a soldering iron while replacing the transistors. This causes them to go leaky and then (later) go short circuit. These caps aren't on the circuit diagram so the value is unknown, but removing themn (a) cures the fault abd (b) doesn't seem to affect the output waveform.
Your mileage may vary.