@kevster996 Hi, sorry I just read your post number 3 and can see a lot of info in there that I didn't answer...
The big lump/box straight after the clamp and before the flex section is in fact the Cat. I guess they put it there to make more room for the prop-shaft underneath the car on the 4motion.
I've picked up a new exhaust clamp, gasket, manifold gasket, manifold nuts and turbo oil return gasket for mine, so hopefully it will go on without any leaks. I'll get it mapped at Narco.
I see you fitted a new actuator... these can be really fussy on how they are adjusted on that thread... did you at least use your old one to set it in roughly the same position, maybe you're over boasting? Certainly with limp mode a VCDS scan can tell you a lot. If you're not sure if VCDS would be useful for you, you can try a cheap clone before buying a genuine one from Ross Tech. Even for simple things like resetting an airbag light it's definitely a must (in my opinion) for any VW owner.
Also I see you say "just did egr and cooler delete so a bit of weight saved there!" did you have the EGR mapped out? If not that will throw an ECL, though don't think it causes limp mode.
Try and keep the faith, there's not many TDI 4motions around and the MK5 is a great car to upgrade and tinker with. I've had a front end knock for 3 years and still not got around to fixing it.
Good luck
Stu