For most of us that have done this, pictures would be like reliving a nightmare! lol What fuel line are trying to unhook? If you cant get the outlet side of the filter to fuel rail line off, disconnect it at the fuel rail itself. Once the head and intake are off then you can resort to large tools to break the torque on the banjo bolts.
The missing exhuast stud is a common issue although its usually one of the studs on the far side of #4. Just get a replacement and thread it in. I always pull the exhuast manifold off the head, leave it attached to the downpipe and after removing the bellhousing exhuast brace clamp...pull it to the side out of the way. Upper intake has to come off regardless in order to get all the electrical disconnected. But save yourself alot of time by pulling the head with the lower intake still attached. Make sure you disconnect the heater hose from the hard pipe that wraps around the head. Quick way around the A/C and PS without unhooking the hoses, unbolt from their mounts and tie off to the inner fenders. Leaves plenty of room to work. As you said you are doing- Take Your Time and do it right the first time. Should be a piece of cake, and once you get ready to bolt it all back together you'll be an old pro!
~Darin <img src="/forums/images/graemlins/baby.gif" alt="" />