I did mine with vocky's method (used the WeaponR's Y-piece), and it did work ok, although welding the flexis on so they sealed well was a bit of a PITA. If you do it that way i'd suggest leaving some stubs of pipe sticking out of the flange and then stick the flexis over them and weld. It's also handy because if you put the flexis flush with the flange, it gets difficult to bolt the flange up.
I think it's worth considering bending the 2:1 pipe. Biggest problems I had were sealing the Y-piece and the 2 upper flexis. If you can get around that it would save a lot of time (and money - I think the 90 degree bends were £10-15 each, as were flexis).
I opened up my OEM backbox to 2.5" and removed some baffles then welded it back up - that seemed to do the trick quite well. OEM backboxes go on ebay for around 99p so it's worth a punt. As before, if you sell your milltek backbox too you'll likely end up with a full WeaponR system AND some money left over 🙂
edit: I used one of these cats:
http://www.nemesisuk.com/mm5/merchant.m ... CONVERTERS
But I had to grind the edges down a bit (they're just spot-welded for the heat shield) and put the cat at 45 degrees. All a bit of a pain really, but it will fit... Not sure how much extra airflow you get over the one you guys are suggesting though.