Yeah, that's kinda ugly - no offense.

You get a star for using a KML file. A KML file can produce maps with much more info than a GPX file.

I opened your KML file and looked at its contents. You have a <LineString> tag followed by lots of coords. That's good. Those coords will draw the line you want to see on your map.

However, your KML file also has a gazillion chunks that look like this:
<Placemark>
<TimeSpan>
<begin>2011-04-03T08:00:43-07:00</begin>
<end>2011-04-03T08:00:45-07:00</end>
</TimeSpan>
<Style>
<IconStyle>
<color>FF00FFFF</color>
<scale>0.9</scale>
<Icon>
<href>http://maps.google.com/mapfiles/kml/shapes/placemark_circle.png</href>
</Icon>
</IconStyle>
</Style>
<Point> <altitudeMode>clampToGround</altitudeMode> <coordinates>-117.80387755483389,33.60310949385166,286.0</coordinates>
</Point>
</Placemark>

That's bad. The above KML commands add a marker to your map. Your KML file adds a gazillion markers to your map and that is what you seeing.

It looks to me like you want to start deleting lines with line 91. Be sure to keep any closing tags that you need at the end of your KML file.

When you made your KML file, here's what happened.
1. All your track points became a KML <linestring>. Good.
2. Each of your special waypoints became a <Placemark>. Good.
3. Each of your track points also became a <Placemark>. Bad! <== Can you turn that off in whatever software you are using?

Joseph