how do you handle updates to the script (that you make on your own) as well as if we need something added to it specific to our needs.
When you make an update to the script do current users get a free upgrade? if yes how long a time period do we get upgrades (ie.. 6 months, 1 year, lifetime)?
We try to permanently add features to the scrips that we find useful. We are also looking for feature requests and feedbacks from our customers and we consider every feedback and suggestion when we add new features.
Also, all customers will get free updates for life. However, we might ocasionally relese separate add-ons and templates, that will not be free (although not expensive either

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and the second part if there is something that we want the script to do in particular that we don't want it to do for everyone are we able to make modifications ourselves to suite our needs or will you make custom changes for us?
The script itself is made in a manner that allow you to use your strategyes and creativity. You should also be warned that because of his power, it is pretty easy to abuse it. (like create 50.000 blog and ping them daily, every few minutes)
Sources are encoded with Zend and you will not be able to make any changes.
We not had yet requests for custom changes but we can handle it. However, this is not going to be free. You know.. time is money...