> <!-- ERROR : UNABLE TO FIND HTML FILE, USING INTERNAL ONE 

Hmm, never seen that before.  What version of HTTrack are you using?  Also, do
you have "Make an index" ticked?  (Options > Log,index,cache > Make an index)

I did a quick test using v3.20 RC1 and my project index.html file looks fine. 
It points to all projects like "myProject1/index.html" and
"another/index.html"

Also, I don't see any line wrapping..