Well, you didnt mention a brand, so since i've got MAC i'll talk about them...
You're gonna want to unbolt the motor mounts and lift the engine up as high as you can. I ended up just unbolting the tranny altogether and lifting the motor out as far as it would go with everything else still attached...it made things MUCH easier in the end. As for clearance, you'll have to disconnect the steering shaft, which will then run between 2 of the header primaries, and there's an issue with the clutch cable coming really close to the headers, so you might want to pick up some heat shield wrap or buy a cable for an SN95-year Mustang because they're longer and will give you more clearance. Other than that, just make sure your plug wires are nice and tight on the plugs so they don't slide over and tough the pipes and you'll be fine.
As for the bolts to connect the mid pipe to, MACs come with all that, so you might want to give the manufacturer a call. As for plugging the O2 bungs, get an 02 sensor and take it to a hardware store and match up the depth and thread pattern with a bolt and use those. A lot of people just use old 02 sensors...i did.
Hope that helps. PM me if you've got more questions.
