Many thanks Reino for all your information! Today I improved my station grounding in the shack. My grounding outside is good, three 2.4 meter ground rods that are 2.4 meter apart and close to the shack. I just increased the size of my copper buss bar pipe behind the radio and equipment to 25 mm diameter and the copper strap to the ground rods is also 25 mm wide. I even built a simple conducting pad for the computer to sit on. I wish I could think of a better ground connection for the computer but there is just nothing to screw to!
The connection between my computer and the radio is a high quality shielded Tripp Lite cable with built in ferrite at both ends and I have the 2 meter long cable passing through a ferrite (#31) torrid with 9 turns. I think everything is pretty will grounded but I think you are right and my end fed antenna is to blame. I think I remember that things worked ok at low power but quit working at 100 Watts. After a computer and radio reset things started working a couple of times but now I'm thinking the radio might be damaged.
The radio works fine on HF for SSB and AM modes and VHF/UHF for all modes. It just won't transmit on FT8. It receives and decodes fine on FT8 though. I don't think the computer is damaged because it seems to work fine (I'm on it now) and I downloaded WSJT-X on my wife's computer (identical to mine) and the radio still won't transmit.
Today I added a 4.3 meter (10% of 40 the meter band) counterpoise with a hose clamp to the SO-239 connector at the antenna and still the radio did not work even at 5 Watts so I'm thinking the radio is damaged. I might try another antenna but I doubt I'll get it to work. I think I'll need to send it back to Yaesu but at least it's under warranty still. I live in the middle of a large city (Houston, Texas, USA) in a single family house on a fairly small lot so the end fed antennas are really easy to work with and very stealthy but I'm not so sure about them anymore. I have had no problems at 100 Watts with any phone mode (I don't do CW) but I have never done anything digital before now.
I quickly looked at the two papers above and they look really good, I'll read them! Many thanks for all your help, I've really learned a lot here. I am an 'Extra' class ham here in the US but I took all three level ham tests quickly one after the other so I'm actually a very new ham and still learning the basics. Many thanks for all your help!