sed ' s/ *[=;]"* */="/g;s//" /2 #first sub-out spaces; for "
s|\(.*M\) \(.*\)|\ #then do the replace
<wpt \2">\
<time>\1</time>\
</wpt>|
' <<\INPUT
11-06-2014 - 10:49:06PM lat = 41.858657; lon = -91.345142
11-06-2014 - 10:49:49PM lat = 42.864653; lon = -92.349914
11-06-2014 - 10:50:35PM lat = 43.874808; lon = -93.350364
11-06-2014 - 10:51:21PM lat = 44.885047; lon = -94.350058
11-06-2014 - 10:52:08PM lat = 45.895078; lon = -95.349920
11-06-2014 - 10:53:30PM lat = 46.905178; lon = -96.349837
11-06-2014 - 10:54:50PM lat = 47.910303; lon = -97.350606
INPUT
This is what I came up with. It's fairly simple in sed. I use literal characters here because it is easier for me to read and because not all sed's will handle backslash escapes in the right hand substitution field. If yours does, then feel free. Anyway, definitely those inline comments will muck up any sed so do remove those before testing.
###OUTPUT
OUTPUT
<wpt lat="41.858657" lon="-91.345142">
<time>11-06-2014 - 10:49:06PM</time>
</wpt>
<wpt lat="42.864653" lon="-92.349914">
<time>11-06-2014 - 10:49:49PM</time>
</wpt>
<wpt lat="43.874808" lon="-93.350364">
<time>11-06-2014 - 10:50:35PM</time>
</wpt>
<wpt lat="44.885047" lon="-94.350058">
<time>11-06-2014 - 10:51:21PM</time>
</wpt>
<wpt lat="45.895078" lon="-95.349920">
<time>11-06-2014 - 10:52:08PM</time>
</wpt>
<wpt lat="46.905178" lon="-96.349837">
<time>11-06-2014 - 10:53:30PM</time>
</wpt>
<wpt lat="47.910303" lon="-97.350606">
<time>11-06-2014 - 10:54:50PM</time>
</wpt>
