Hmmm .... It appears like you've managed to modify your Yaesu FT-101E into a Basket Case of Problems/Failures. I have not read anywhere in your Posting that you have the required Tesr Equipment & Yaesu Service Manuals, Oh but you have mentioned something about having a Golden Dittle Stick and tightening down all of those loose Capacitors.
Yaesu Service Manuals:
Did you know that if a transmitter is Self Oscillating or Flying, you will never see Full RF Power Output because the transmitter is covering a multitude of Frequencies above and below the Carrier Frequency. It can be Plus & Minus 30 MHz .... a major headache trying to troubleshoot and locate the defective components! Till you solve the Transmotter's Self Oscillating, Flying or the Power Amplifier's Stage NOT Being Properly Neutralized, you're going to continue to Shotgun Analyze the Failure.
Hint #1: NEVER ASSUME that NEW / NOS Cannot Be "Bad From Stock" Components!
Hint #2: NEVER ASSUME that Silver Mica Capacitors Are GOOD Because 99% Of The Silver Mica Capacitors "FAIL" At Higher Voltage Levels!
Hint #3: Poor and/or Cold Solder Connections On Vacuum Tube Finals CAN Cause Self Oscillation In the RF Driver & Final Power Amplifier Stages!
Hint #4: In The 1970s & 1980s (Even Today) Amateur Radio Dealers ALWAYS Sold 6JS6C Matched Pairs Of Vacuum Tubes For The Yaesu Products & Big RF 1.5 KW Amplifiers (Using 3-500Zs) Because It Causes LESS Problems With Self Oscillation / Neutralization! The BEST Method For Testing Vacuum Tubes For Gain Emissions Is Either Have A Military Surplus Tube Tester Or Know Someone That Owns One.
Hint #5: When Ceramic Bypass Capacitors Become Defective, They Normally SHORT And They Can Be Read With A DMM On The Lowest OHM Scale Indicating Between 10~40 Ohms And The Capacitor NEEDS Replacing!