Homebrew PCBs

I'm marching down another path to plot circuit
boards directly on copper.
The .020" pitch TQFP part with the .008" tracks
is pushing the limits of the plotter pen.

There are "fat spots" in the trace every time the
pen touches down.  And protel 99SE likes to break
up tracks and touch the pen down a lot.

No problem.  I wrote some code to read in the gerber
and combine sub-tracks with common beginning/end points
into a single track that gets plotted without
lifting the pen.

Problem.
When you clean up a protel board, there's a feature
that lets you dynamically reroute a track by just running
a new track segment from any two places on the existing
track.  It puts in the new segment(s) and removes the old segment.
  
But in manipulating the gerber, I discovered
that the end of one segment is not exactly at the same point
as the beginning of the next.  There are actually a lot
of gaps in the tracks.
Looks ok on the gerber plot because the aperture covers up
the joint.
But I can't figure out how to determine track continuity from
the gerber...without doing a LOT of extra work to find stuff
that's "near".

Am I just doing the board cleanup wrong?  Or maybe some automatic
cleanup pass that I've not yet discovered in Protel 99SE?
Everything automatic I've found insists on rerouting the whole
board and messing up all my hard work.

Suggestions?
mike