As mentioned, just go slow and label things. What I normally do, even after doing several engines now, is to follow a manual (Haynes or Chilton's are fine), then take my own notes as I go along. Such as, if I take a part off the engine, and it has several bolts of diffrent lengths, I will take notes and even draw pictures on which bolts go where. If I can, I will tape them in their respective places on the part itself. I will also take many digital pictures before and during disassembly.

I just did the headgaskets on my '95 3.0L. It's the second one I've done. I didn't really follow a manaul this time until I got to the reassembly (for torque specs and timing belt installation procedure). I took several pictures and took 4 pages of notes (both sides). I followed my own notes on reassembly with exception of what I just metioned about torque values.

Another big thing that helps me--using a fishing lure plastic box to store bolts and small pieces in. I'm referring to those clear boxes (or with clear lids) that have various size compartments in them, often with removable dividers. I then put masking tape in strips across the top and label which compartment is what, and what step it is in my notes.