Man I didn't have to cut anything to fit the pedal box in it bolts straight in. If you mean the holes for the clutch master that was easy.
Thanks to this dude on Rollaclub. That bit above where the clutch line came through I just cut it off completely as I thought it looked tacky hacking a chunk out. Then you can see next to where the brake booster mounts that indent where the clutch master sits perfectly drill the holes and then use a dremel to elongate the holes if you're off a bit. You can get the pedalbox in without taking out the whole dash pad too its a bit of a bitch but I managed.
You see that so called tube the previous owner put in thats for a catch can. I wouldn't have a car without a catch can.
my 2006 xr8 when I rebuilt it at 80,000kms the intake manifold was full of black oily crud and so was all the throttlebody. If you know commodores they have this same issue with the throttlebodies always sticking from the gunk sucked in. My saab is a prime example the breather goes from the rocker cover to the intake tube between the filter and turbo and the turbo was sucking in oil.
Read this about the oil system. The 4AGE has a tedency to dump oil in the manifold in hard left corners.
Put a catch can in run a line from the rocker cover to the can then from the can back to the manifold if you like fill it with steel wool and run a line to where the previous owner put that connection and you're done. Personally I skip the back to the sump bit cause you can run the risk of condensation in the catch can and it mixing into your oil. It takes a long time to fill one so I just dump it when I do my oil change if there it any in there.
As for bearings just see how much movement they have in them the rods will move from the front to the back of the crankshaft a real little but shouldn't have any movement from side to side i.e. engine mount to engine mount.