From what I read, you are doing wrong in my way of thoughts.

In a simplified manner, first off you need to set up your CAD system for line thicknesses based upon colors (and layers).

Then go to the thick line representing maybe the edge of the model surface and activate that.

Then look at the resulting DXF file, zoom into the little line segments SNAP to one, and then pan diagonally down to one further along the model surface and SNAP to it there and let the connect points feature draw a line. This line, when shoved through your plotter will then automatically come out thick, like .050"

Do same for interior lines, but use different color (or layer).

After you create a few of the new long line, the just erase off the helter-skelter little crooked lines from the DXF file that WinTopo created. It will bit by bit then reduce your file size.

Those little crooked lines are trying to create a line thickness by multistroking, and using your thinnest pen.

I work with 10-12 foot long scanned drawings quite often, and it takes a lot of RAM to process the drawing in WinTopo, not a fast processor. I began by using their version 1.10 and am now using 1.67 And those big files created by WinTopo for me are about 150 Meg each, but eventially get reduced to about five when near completion.

Wm.