Thanks a lot for your help Amber! I went to Cardiff PEO today and my wife's application for Settlement was approved! Hurray!!
The staff were quite courteous, the least you can expect when you pay ~£1500, and the application was processed in about 1.5-2hours.
Documents I took:
Cohabitation documents - Several Bills in joint names, a few bank statements for each of us (individual accounts), a few of my recent payslips and Driving Licences.
My ILR BRP and wife's current BRP (which was obviously withheld afterwards).
Oh also took Marriage licence/certificate from Pakistan.
Filled out application form.
I took photocopies of everything but they basically said they dont need them, they'll make their own copies of anything they want on record.
Thats it!
If you're thinking of going to Cardiff PEO from outside Wales I would highly HIGHLY recommend taking an early morning appointment so you get to Cardiff early, say before 9am, with none of the Newport traffic otherwise you'll be teetering along at 10mph on the motorway despite taking the Toll bridge, costing £6.40!! (had no idea it was going to be that expensive)
Good luck to all, I'm finally out of the race!