Brakes pipes are easy to sort, emissions might come down enough if you take it for a good run and get it hot just before its due for testing, the welding can always be sorted just depends how bad it is and how much time and money you want to spend
First thing is note the codes down and then clear them, then see if they come back on, they dont seem to point to a misfire. If you've changed plugs, leads, coil make sure you have firing order correct if so so try compression test
You've done better than me ,I've managed to snap a few, but at least I've not bust the trim but then plan to have it on road this summer has changed a little πͺπͺ
It's been a long slow process as it wasn't just the outers, when the sills are finished I'll have used 2 sheets of 3x2 and 1 arch repair panel (thanks savage).
But I can now see light at the end of tunnel, just hope it's not train coming π―