Great thread
1) Magnetic trays for the bolts/nuts during disassembly. Put all bolts and nuts back into place if possible, if not, wrap them in tape and tape them to the part or put them in a bag and attach it to the part (zip ties work great for this - you can zip tie/tape the bolt beside where it goes or put them in a bag, zip tie the throat of the bag and then attach the zip tie to another zip tie around the part - I use zip ties because sometimes tape leaves that sticky residue or it might be in a place where you don't want to use tape). For example, zip tie all the head bolts in a baggy and then zip tie that bag around one of the spark plugs that is screwed into the head or through one of the head bolt holes. For an even better idea, see #2 below.
2) Scriber or engraving tool - makes permanent marks on the outside of things like heads, cylinders, y-pipes, can mark the PTO and MAG TDC's on the Magneto cover plate and on the case for reference etc., so that you can reference these when re-assembling. i.e. mark on the cylinder - "PTO" on PTO side cylinder and PTO side carb etc. Makes it simple for re-assembly. You can use a felt marker, but if you put your stuff in a parts washer or similar, say goodbye to your reference marks. A center punch works good for reference points but an engraver is nice becuz you can write things like squish clearance/base gasket thickness/etc., on the cylinder itself so you remember and its right there. You can also engrave numbers on your bolts and then a number on the case/head/whatever where it came out of so they all go back in the same spot. Also you can mark things like "this side out" or similar so that you know which side of a domahickey faces out or in or towards the front or back of the motor or wherever.
3) For the coolant thing, just take the muffler off, get a fuel siphon hose, plug one end in the coolant tank, drain thru the muffler hole in the bellypan into a pail/whatever on the ground. The siphon effect will work so long as the container is lower than the siphon point. Once the coolant tank is empty take the hoses off, push the siphon hose in the coolant line, siphon more coolant, etc., keep working down the motor taking lines off and siphoning until you get to the lowest point. I usually only lose about a 1/2 cup of coolant this way when I take the final water pump hose off, couple rags underneath and its soaked up, no spill, no mess, don't have to clean out my shop vac.
4) as stated, take lots of pics, keep a log book and write everything down or draw diagrams, especially in areas where you can't take pics and just in case your camera falls in a puddle before you get them downloaded or the wife deletes them by accident, etc. Its good to take notes as you break down the motor/whatever down. Especially things like timing BTDC, clearances, run outs, etc. Its good to know that you had three spacers on your secondary clutch, but its even better to know that two of them were on the outside and one was on the inside, or two on the inside, one on the outside, etc. A quick note or diagram will save you some head scratching during re-assembly.