Yep, link then out.  The R8 does not allow you to program them as unused, I think the Excel does.

The panel usually comes with links fitted, they look like little U staples.

I would always advise using magnetic contact on the entry doors to initiate the entry delay, having the PIR's on inhibited entry is required.  This also works far better for exiting the building as the exit time delay is cancelled once the door is shut, allowing you to confirm alarm sets without having to wait until the exit time has passed.

Inhibited entry on the PIR means that the PIR will cause an immediate alarm when the system is set EXCEPT if the system is in entry mode - if some one comes in through a window, the alarm is triggered immediately.  If you open the door and then trigger the PIR, nothing happens, entry timer continues as normal.

It would work, but you would be far better running all the PIR's on their own zones (7 zones), and then having the last zone daisy chained for door contacts.  

Set all PIR's to guard, except ones which can pick up movement on entry exit, these would be set to inhibited entry.

The mag contacts would be set to entry/exit.

It is considered bad practice to daisy chain detectors unless they are of the latching type (very old fashioned), the reason being you are unable to tell which detector was triggered and caused a genuine or false alarm.  Fault finding would obviously be a nightmare!

I would probably not put a keypad upstairs either - you usually have a keypad at the frontdoor/bottom of stairs, with a PIR covering this area (usually set to inhibited entry due to front door), this PIR then reverts to entry/exit when part set, and the door contacts revert to guard.  Th upstairs zones are ommited from the part set suite.

At night, you enter you code, and leave up the stairs.  The exit tone expires and the system sets.  Your safe upstairs with downstairs protected.  In the morning, you walk downstairs and the entry timer starts......

Part set entry/exit tones are quiet and can be muted.

The install guide just shows it to give you the option, should you have more than 8 zones.

Although, if you had more than 8 zones you would usually opt for a system that can be expanded to accomodate more.