I have just gotten into this, and have tried a few different ideas.

I have found that taking the engine apart is the best way. I disassemble it as far as possible, but at least take the back plate off and the head off.
If you can pull the crank even better. I then take all the little parts and put them in a little stainless cup, fill it with prestone antifreeze and put that into the crock pot full of antifreeze.
I cook it on high for at least two hrs. and up to 4 hrs. I then pull out the stainless cup, drain all the antifreeze out into the crock pot as I can, and then take it to the sink and flush with water.
After it has cooled down, which takes just a second, I get a tooth brush and brush the parts under the running water (remember to screen the drain). Sometimes I will use a little soap if it looks like there is a little oil film still on the parts. Just look at the brush and you can tell if you need a little dish soap on the work.
If the parts are not coming clean with just a little brushing they need a little more cooking, so back they go for another two hrs. This rarely happens and is mostly the heads which seem to suffer no ill effects even if left for a long time in the crock pot.
The parts come out like new, and I mean really like new. It is really remarkable.

Problems can occur!! One thing I have found is that anodized parts suffer, and so do plastic parts, such as the plastic housings found on Cox TDs. The paint on your old green head will be gone also, so if you use this method you will have to repaint it.
I also do not use this process on carbs or glow plugs. Although it will work on all metel parts, I have found that the rubber and gasket parts on carbs can be at risk, also the carbs don't usually have fuel cooked on and can be cleaned with fuel and then soap and water.
The glow plugs probably could be cleaned, but at $5 apiece why take a chance.

After the cleaning you have a unprotected engine and all the parts need a coating of oil. Some use WD40 to displace water, but I just blow them out with compressed air and oil them. but them together and test fire them. It will warm them up and get rid of all the water. I then add after run oil and put them into zip lock bags.
You could also heat them with a blower, like the one used to shrink monokote, and dry them to store as extra parts.

I have found that if you don't take the engine apart (at least the head/glow plug and back plate, that a lot of junk gets left in the engine no mater what kind of flushing you do. If you don't get the sleeve and piston out, you must really flush out the block and make sure nothing gets left there.

You can use the antifreeze until it looks so dirty you can't imagain it working, and then it is off to the recycle bin. I did all the engines so far in one bath of antifreeze and have a half gallon left.

I have had a great time cleaning my collection, and I started with the most hopeless of the bunch. Man did they look good after the bath.
Good luck
MR Flyer57