Hacking Computers

The way that hacking bonuses stack is being slightly modified in order to accommodate the new mainframe systems that are available.

Using a neural jack and using a computer no longer stack. This is important for people with hacking computers that give a +2 to hacking attempts, as these will no longer provide this bonus if interfacing with the system with the neural jack. Advanced hacking software (+2 to hacking) can be used with both a separate computer and with a neural jack.

When hacking a remote target over the WDN the size of your connection will affect the hacking bonus you receive from a computer or neural jack. If using a wireless or domestic connection, you will not gain any bonuses from your computer/jack because there is not enough bandwidth to take advantage of them. If using a business level connection (most small businesses have these for their database and sale systems) then the bonus from these systems will be up to +2, not including hacking software and internal A.I.
If using a Corporate level connection, as used for Corporate and UIG database systems and research computers, you can get your full bonus from your computer/jack.

For example:
Agent Smith has an intelligence + A.I & Computers score of 18. His internal A.I is level 6 and he is using a mainframe system that gives a +4 bonus to his hacking attempts. He is using Advanced Hacking software and a business level data connection.
His mainframe is limited to a +2 bonus due to the business connection, so his target to roll under is: 18 + 6 (A.I) + 2 (mainframe) + 2 (Hacking software) = 28

Agent Doe has a neural jack and an Intelligence + A.I & Computers score of 18. He is also using Advanced hacking software and has a Corporate level data connection. His internal AI is also 6. His action total is: 18 + 4 (neural jack) + 2 (hacking software) + 6 (A.I) = 30

There are also advantages that mainframes can have that further increase their capabilities, but these are not common knowledge.
Prices and further details about mainframe systems will be uploaded to the WDN in the future.

WRT internal AIs, what downtime action is it to upgrade them?

I believe a free action, as with other purchases.

Free action is fine, though as with most things, using a minor or major action may get some extra benefits, or it may not.
Upgrading your AI as a free action, for instance, is seen as buying up some new modules from the WDN. Using a minor or major action would be training it yourself or spending a lot of time upgrading the programming to your own needs.