Hi Koe,
First thing to understand is that Mobile Kit Pro is for smart phones like iPhone, Android Phone, and Win 7 Phone. It is not for iPad, as mentioned in the Mobile Kit Pro product page we feel that iPad with its larger screen should be able to use the main site skin.
In answer to your questions:
1. You will have to test that yourself to determine if your custom features are mobile friendly or not, and you may need to implement alternate renderings if you find they don't currently work well. In mojoPortal features we had to implement some alternate rendering options for some features that are controlled via theme.skin settings to make markup renderings that are more mobile friendly.
2. Technically it will work in .NET 3.5 in Full Trust hosting (but not in Medium Trust which is used in most public hosting), but you may have to comment out one thing in theme.skin that sets a property not supported in .NET 3.5. My advice is to go to .NET 4, it has been out for a long time now and we won't continue supporting .NET 3.5 forever in mojoPortal. When .NET 4.5 ships later this year we may change to only supporting .NET 4 and .NET 4.5.
3. The minimum mojoPortal version required is 2.3.7.0, so you will need to upgrade to use Mobile Kit Pro and you may as well upgrade directly to the latest version.
4. If the servers are owned and directly managed by your company, yes, if you are deploying your clients to their own servers or shared hosting, you should instead buy a single installation license for each installation.
Best,
Joe