Check the motherboard memory sticks, maybe you dislodged one when you were re-seating the other boards.
If the floppy doesn't work, check the CMOS settings. Look at the memory settings and the drives settings. Bad CMOS usually means bad battery.
The Invalid GraphFile Path error means that the control software doesn't find the location for the graph file as listed on the 4th line in the PATH.DAT file. Frequently a lack of enough memory to create a RAM drive causes this problem.
You need to resolve this issue before you can look at the E-Stop problem.