With steel rods .040 to block is fine. With aluminum rods .060 to block. same with cam too.
You can carefully tape up the piston top take up slack and also keep it from scuffing the cylinders, With a rod using cap screws (Bolts no nuts) You can hold block to the side or where piston will not fall back out, and instal a upper rod bearing in the rod, install carefully not nicking the crank and next we will get a little wild and crazy.
Install the cap screws by hand but tighten them deeper into the rod than the cap would allow. Be sure cam is not in block at this stage. With the bolts in the rod too far hold the piston pushing it toward the crank as you rotate the engine.
Watch each bolt head one cylinder at a time to see exactly where the bolt head clearance needs to be. mark that on the block pan rails with a marker across the pan rail. This helps prevent you from grinding or cutting the block in the places you do not need any extra clearances. By doing this in this way you will see exactly where the closest places will be. after you have a spot marked on the pan rails to line up with bolt heads, Nothing wrong with marking this spot with a scribe if preferred.
Remove bolts and install other rod bearing half in the rod cap and install the rod cap. Rotate engine slowly and watch to see if it clears, and by how much or if it does not clear and by how much. write on the pan rail or a hand drawn replica of the pan rails the appx amount you think it will need to be cut to get the .040 + clearances in all places.
Remove piston and rod and tape up or completely remove crank. To me it is easier to tape up.
.Clean oil off of crank rod journals and wrap with a tape to completely cover the rod journals for a pretection against the flying hot debris from the cutter or grinder.
Cut carefully but cut in only the places where you marked to be cut.
This will be a trial and error process and is a pain in the butt but it is necessary. For me I have found that a grinding round or triangle stone in a die grinder or high speed rotary grinder works better than using a carbide cutter. Maybe you will prefer the carbide. Hold the cutter or cutting stone straight and verticle as you cut.
After the pan rails seem to be cut enough for clearances, use a straight edge on your marks like a tri-square and eyeball on the bottom of the cylinder walls where notching them also will be in the same plane of travel of the rods and rod bolts. That will alce need to be ground or cut for clearances.
Is anyone starting to get an idea why we charge a few hundred to do stroker clearancing?
This process is a little quicker and easier if you own fixtures for each stroke size made by BHJ but they are costly.
The bigger the stroke is, the more material will need to be cut out of the block in three places for each cylinder.
4 inch stroke with a 350 or 400 is about the maximum. I prefer the 3.875 as the maximum.
If you are careful and sneak up on the needed cuting amount and cut in the correct places you will not hit wateer or oil. If you do cut through into water, cut farther and get it welded and do a bottom block fill with Hard Blok and you should have no problem once you again grind the weld so you have clearances you need.
Whew'
Ed