Corrosion pitting on the deck can be sealed at head installation and can be honed easily with a large oil stone. If you have concentrated pitting in the cylinder bores you will have to re-hone for sure. To get a good crosshatch you'll have to have the pistons at BDC or remove them to keep the cylinder walls straight. If pitting is too deep to remove easilly, you'll have to judge whether your piston clearance has been exceeded. A badly pitted area close to the top of the cylinder can cause a loss of compression right out of the gate.
You'll have to be the judge whether to go back to the machine shop or not. I just pulled one appart that I had in storage for better than 20 years and the cylinders were OK. I used SAE 140 gear oil on them when I originally put it together and it had no signs of rust at all. I was really surprised. Even though it was stored in Kansas where rainfall is pretty scarce, I expected to see more corrosion just due to the amount of time that had lapsed.
Kerby