Thanks for the reply but this has all been a tragic problem magnified by myself. Here's the general run down.
This is a standard Wilson II printer received about 3 weeks ago. It's got the standard direct drive etc.
Once I got the machine working, I started going through the steps of calibration. My filament was standard PLA, I measured it 5 different places and it trued out at 1.74mm
I got to the extrusion calibration and kept missing by between 30 and 40 mm short. So I cranked up the esteps till I could consistently get 100mm .. many prints went by just fine even though my esteps was sitting at 139 / mm. What did I know I was making prints that didn't look bad and life was pretty fine.
All the micro step switches were in the position they were set in from Marty. I didn't know enough to touch them. I changed out filament and tried printing out a part I'd designed for a friend. And the dimensions were off and the thing looked over extruded.
I checked the extrusion and it was somehow short again. I started to think I might have the wrong microsteps so I pulled off the A4988 driver and looked and it was sitting with all switches in the on position. like every other driver.
When I put the driver back in I got no extrusion when I tried to check it again, and doubt ran through me, the position I put the driver in seemed right but the silk mask put the board being 1 pin higher than the rest of the drivers. I should have sought reference. I should have looked at it good before I took it out. But I was in a rush and went eh maybe I missed. So I put it in 1 pin higher .. right where the mask said E0 here (more or less.) Powered it on and let the good times roll, the magic smoke was everywhere.
So there's a good lesson, never fuss with a 3D printer unless you're 100% certain. As it turns out the reason I had no motion when I tired it before was because the extruder stepper motor connecter had come off the Pica board.
As best as I can tell I have fried 3 drivers, the Mega 2560 and possibly the Pica board.
Add insult to injury, in my analysis and testing aka Autopsy I reset the esteps to 104 and the thing heats up and extrudes exactly 100mm or 50mm or whatever I want mm.
I have a Pica on order and a new Mega 2560 and I may be able to get my hands on a few drivers and/or a Ramps board.
I'm wary of putting in a ramps board because I know that means I have to fuss with the firmware again.
So I may suffer no printing till I get all the pieces and put my printer back in order.
I do not know why I was under extruding and needed to crank up the esteps so high. And I don't know why suddenly I'm flooding my build platform with plastic.. but It all has been educational and I'll take my lumps. I probably had it too easy putting together the Wilson II. It went together like it was designed to.