Make a bunch of drawings before you start. With many dimensions of everything. Measure from reference points that will remain as well as dimensions that will be lost when cutting starts. You can not have too many dimensions. Measure everything. You can draw pix or you can take pix and add dimensions. You need lots of pics also in case you forget what overlapped what or how something was attached, etc. Doing all that will save your butt months from now. As Kevin mentions you can add scribe marks or 1/8 holes thru two pieces or any method to add reference or alignment registration.
With hood hinges and door hinges, (and any other critical position component), I drill two offset holes in each hinge, far apart, thru hinge and mounting surface, (firewall/A pillar/etc.) before unbolting. Then on reassembly, I use two 1/8 drill bits as temporary guide pins, bolt it up and remove pins. This is, of course, if the hood or doors or whatever, has a nice fit to start with. Either way it gives a baseline location for the "was " condition.
