Those passages go across to the other side at a 45 degree angle (+/-).
I was able to see where they passed by seeing the "hot spots" on the cylinder walls.
I used a long drill bit by hand to clean the crud out of there before I sent her to the shop.
After she came back I checked them again, and blew a ton of air with different tubes, etc, all over that damn water jacket. There's a lot of crud that needs persuasion to get out of there.
Nice work bro! I just went through all this stuff last summer/fall/winter. Hope yours goes at whatever pace you desire. I was in no hurry, and got tired of hearing "got it running yet?".