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Answering all the questions at once.
The reason why NYTimes does not work with MSIE cookies is that JPluck does not write new cookies back to the cookie store. Apparently NYTimes sends a new cookie value during downloading that it wants to see when you download subpages.
However, you can pluck NYTimes correctly when you use a Mozilla/Netscape cookies.txt file. This uses a different cookiestore implementation that holds new cookies in RAM. Fortunately, MSIE lets you export its cookies to cookies.txt format. Simply point JPluck to the exported cookies.txt file. I tried this with the TT's JXL and it works fine.
JPluck never writes new cookies to disk. It only holds new cookies in memory while it's downloading the site. After the conversion is complete it discards the new cookies.
Until the MSIE cookie handling is fixed, the best solution would be to use Mozilla just to log in to sites and obtain a cookie. You can still use MSIE for normal browsing.
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