It sounds like you want a simple state machine. You're checking for duplicates and also checking for two parts of a tuple.
No big deal. Here are some hints:

First off, use split(/,/, $_) to break up the line.

Then for converting lat and longitude formats:

 my @latitude = split(/\./, $_[5]);
my $latstring = sprintf("%8s", ($latitude[0] . $latitude[1])) ;
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And finally for the state machine (totally untested):

while (<LOGFILE>) {
chomp $_;
if ($_[0] eq $lastline ) {
    if ($_[0] eq "1sec CDMA Event DtiC(0)")    { 
         #average those things or whatever you neeed to do
    }elsif ( $_[0] eq "Generic Scanner PN Measurement DtiC(0)") { 
         #average those things or whatever you need to do
    }
} else {
    #determine which part of the tuple this line is and 
    #store Rxpower/add Rxpower and massage lat/long into strings 
}

$lastline = $_[[0];
}
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As I mentioned, all code is untested, but it's a starting point.
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