Good job, well done there.
As for running in, just take your time. Try not to give it too much throttle, and don't make the engine labour. I was always told to drive like you have a bowl of water in the footwell. Very gentle for 500 miles, then slowly increase up till 1500 miles. After that, all should be bedded in and up to spec. Keep an eye on you're levels, and temperatures.
Many will tell you that you don't need to run engines in, because modern oils and machining is so good. Load of balls, engines still have pistons and bearings. The technology is the same, so the procedures for running in are the same.
In the end you will have a nice tight engine, with plenty of poke that will serve you for years.
Defiantly get a flexi pipe sorted. You don't want to end up with stress fractures on that new mani. Have you sorted the small bracket near the gearbox?
Cam cover sounds cool, get some pics up when it's done.

Good news on the cam, I'll have to come and have a looksy when she is all done, one of the things on my to do list is the top end. As 866 cams are so rare, I may speak to davies bearings, to see if they can re profile an original for me.
Also need to speak to sparky5 about doing me a throttle body.
You should have a quick little car there when set up on the rr, what are you aiming for 75-80hp?