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Oops yes, lint has picked up that this line:

if( best = 9999999) deststart = cur

Is assigning to best (not comparing), I'd like to propose this solution:

#!/usr/bin/awk -f
FNR==1...

How about this:

#!/usr/bin/awk -f
FNR==1 {file++}
{
day=$1
gsub(/-/, " ", day)
split($2, t, ".")
gsub(/:/, " ", t[1])
x=mktime(day " " t[1]) + t[2] / 1000
if(file==1)...

You could try this script. I believe your OS should come with GNU awk by default so it's much more efficient to use the mktime() feature to convert these times.

#!/usr/bin/awk -f
{
day=$1
...