> 1. the -r is a path level. Can i specify a click level?.

No, no, -r is the click level (number of clicks, from the 
TOP index (index.html))

> Can i tell 
> httrack to load prerequisites(meaning it will get all 
stuff 
> necessary to load the home page correctly but wont get 
html 
> pages beyond -r3.

If you need *only* the homepage, use filters (Options/Scan 
rules) without any depth value:
-* +*.gif +*.jpg +*.png +*.css +*.js

> 2. Say i download www.cisco.com using N3. All files will 
be 
> stored in output dir web/. Now i delete some unwanted 
files 
> from web/. Can i use -x and get httrack to point the 
missing 
> url to a default error page?.

No - the only way to "delete" (exclude) files is to use 
scan rules:
-www.cisco.com/some/unwanted/files.asp*
-www.cisco.com/more/unwanted/directory*

And use "Continue an interrupted mirror"

> 3. Can i set my own error page insted of using httracks 
> error page.

This is not yet possible - as pages are downloaded AFTER 
links are being resolved (and written to the original html 
file) ; but it may be added in the future