To give an update on this issue.
I found the problem(s), as I'm not sure if it was just one or two issues.
When I plugged it in nothing happened, but the Rpi was working fine.
I probed the board for shorts on the atmega and all looked ok and then I looked at the Rpi header and I found that the Gnd and Sck where shorted together. I used my heated solder sucker(I love that thing) and my hot air desolder station and removed the header and replaced it with a new one. So no more short on that.
Then I plugged in the heatermeter and then I had smoke coming from the Mcp1700. So, I removed that as it to had a short between GND and one of the other legs. Put in a new one and all was good, the atmega programmed and I was able to log into the HM and change the settings.
It helps to have a multimeter that has a good continuity checker that beeps, makes finding shorts pretty easy for the most part.
John