I increased the link depth to 3, the log file becomes the following:

HTTrack3.44-1+htsswf+htsjava launched on Sat, 17 Dec 2011 23:01:58 at
<http://cal1.cn.huc.edu/targumbrowse.html> +*.png +*.gif +*.jpg +*.css +*.js
-ad.doubleclick.net/* -mime:application/foobar
(winhttrack -qir3%e0C2%Ps2u1%s%uN0%I0p3DaK0H0%kf2A25000%f#f -F "Internet
Exporer 7.0" -%F DDM -%l "en, en, *" <http://cal1.cn.huc.edu/targumbrowse.html>
-O1 "C:\Documents and Settings\Duane D. Miller\Desktop\Targumim2" +*.png
+*.gif +*.jpg +*.css +*.js -ad.doubleclick.net/* -mime:application/foobar -%A
php,php3,asp=text/html -%A php3,php,php4,php2,cgi,asp,jsp,pl,cfm=text/html )
Information, Warnings and Errors reported for this mirror:
note: the hts-log.txt file, and hts-cache folder, may contain sensitive
information,
 such as username/password authentication for websites mirrored in this
project
 do not share these files/folders if you want these information to remain
private
23:01:59 Info:  Note: due to cal1.cn.huc.edu remote robots.txt rules, links
begining with these path will be forbidden: /cgi-bin/, /.xml/, /.php/ (see in
the options to disable this)
23:02:18 Info:  engine: transfer-status: link updated:
cal1.cn.huc.edu/showsubtexts.php?subtext= -> C:/Documents and Settings/Duane
D. Miller/Desktop/Targumim2/cal1.cn.huc.edu/showsubtexts43e7.php
23:02:18 Info:  engine: transfer-status: link added:
cal1.cn.huc.edu/text_browse.html -> C:/Documents and Settings/Duane D.
Miller/Desktop/Targumim2/cal1.cn.huc.edu/text_browse.html
23:02:18 Info:  engine: transfer-status: link added:
cal1.cn.huc.edu/get_a_chapter?file=&sub=1&cset= -> C:/Documents and
Settings/Duane D.
Miller/Desktop/Targumim2/cal1.cn.huc.edu/get_a_chapterc924.html
23:02:19 Info:  engine: transfer-status: link added:
cal1.cn.huc.edu/get_a_chapter?file=&sub=2&cset= -> C:/Documents and
Settings/Duane D.
Miller/Desktop/Targumim2/cal1.cn.huc.edu/get_a_chapter7963.html
23:02:19 Info:  engine: transfer-status: link added:
cal1.cn.huc.edu/get_a_chapter?file=&sub=3&cset= -> C:/Documents and
Settings/Duane D.
Miller/Desktop/Targumim2/cal1.cn.huc.edu/get_a_chapter88c3.html
...
...
...

-------------------------

These file names are not properly linked within the HTML or PHP files, etc. 
Any suggestions?
--
DuaneM