After redesigning the carriage and building a new hotend I was off and printing. As usual I started with Teacup and every print finished but the machine was noisy at the speeds I want to print at. The results were not exactly what I wanted either, but none the less still good.
RepRap forum about it but no one has responded yet. While waiting to find a solution to the serial error I decided to try hooking up my DIY sd card reader (card slot and schematic) which went terribly wrong. The first symptom appeared when the temp would read 266 so I swapped the hotend and bed thermistors in the firmware and was getting good readings again. But the Y axis and Z axis only moved at about 10% of the speed requested and only move half the distance. I have removed the SDreader and checked all the connection points and there are no shorts or loose connections so it looks like my arduino mega is done. This is going to set the project back until I can sell another set of Prusa parts to raise the money to continue.
Here's a video of the fourth print it ever did. First with the new hotend.
Hopefully it won't be to long before I can continue development.