Tell us exactly what you want to do, and how you do it -- you are certain to get an answer. Sounds fairly routine to me -- we don't use new, cool or rating, so we don't build the pages. We don't use jump.cgi either, so links can never be cool in the first place (if you want to cut down on CPU usage, eg: on a shared server, dropping jump.cgi is a very good neighborly thing to do).

One thing you can't do in the current release is remove the unused columns (isPopular, isNew, Rating, Votes) from the Links table -- so don't try that, you will have to re-install. Even though they serve no purpose, the script won't run without them.

All three hosting plans at http://www.valuehost.co.uk/hosting/ offer Secure Shell and Cron, so you have everything you need to run nph-build.cgi --all at regular intervals (eg: 24 hours). You just need a few simple edits to nph-build.cgi.

I don't think there is much you can do to increase "speed of building" -- disabling new and cool won't make any difference that you will notice. It depends very much on what else the machine is trying to do at the same time. If you are on a low-budget plan with "Unlimited Monthly Data Transfer", that could be a lot of activity.