mt500ish,
It's more than just how much you need to take off the piston. Is your piston .15mm above the deck? IF not then do your math and get there. Then you'll know how much of the piston needs to come off. If the compression is still too high then you'll need to dish the piston some more and cc it and possibly use a thicker Head Gasket.
I did a quick calc of your math using the 138mm rod for you and it shows a compression height (CH) of 28.15mm. That is the minimum you can go. I'm not sure what that makes the S50B30 piston's crown thickness like, but a brand new piston manufactured at 28.15mm CH is ok. Now it depends on dishing the piston and Head Gasket for compression.
211.5 - 45.5 -137.85 = 28.15
135mm rod: 211.5 - 45.5 -135 = 31 This one may be a better option for you. Talk with your builder friend.
Maybe this will help. Just remember this is for an 88mm crank not your 91mm. Plug in your numbers. Also I just read your post and you already decked the block another .5mm so do all your math a couple of times.
Example:
Stroker Crank 88mm
Combination for Rod and Piston with (M44 1.9L Head Gasket)
Compression Height of Stock US S50 Piston is 32.8mm with Honda 1.8L VTEC B18C (GSR) 138mm rod
Desired Compression Height = Block height - (Stroke/2) - rod length
Desired Compression Height = 212mm - (88mm/2) - ((138mm[Honda rod]-.15mm{protruding out of block}))
Desired Compression Height = 212mm - 44mm - 137.85mm
Desired Compression Height = 30.15mm
The DCH is a desirable height.
30.15mm = 212mm - (88mm/2) - 138mm -.15mm
This tells you that your target compression height is 30.15mm and we have enough meat to shave off 2.65mm from the 32.8mm

Rod needs small end bushing to be drilled to fit 22mm S50 pin.
To get the right compression of about 10.9:1, I dished the piston about 7cc's and used the M44 HG that was thicker 2.04mm not the 1.74mm.
I hope this helps you. Good Luck. Talk to your builder friend and let him help you with the math part of it. Or find some place online to do the math.
Cheers,
~Ralph