I'm finished pocket porting and polishing my Merlin cast iron heads. ( About 50 hrs. labor ) and have 3 spots where there are pox marks in the castings. I have taken pick and scratched at them and can't tell hiw deep they might be but I don't want to grind them out as it will be much deeper than I want to go. My concern is that I'll get the motor together and develop a leak. What should I do? It may be fine as is but as you know when you put so much work into something you hate to have to worry about it when your done. Any help or suggestions will be appreciated.

You don't want to grind out all the imperfections or casting irregulatries.
All you will do is make the ports bigger & that is not a good thing.
It sounds like you are done!
Even the hi dollar CNC heads will sometimes have places in the ports & chambers that the program has missed becouse of "low" spots or casting irregularties.
If you wanted to get real anal about it you could fill them with 2 part epoxy & clean them up but I would just run em' ;)

Thanks, I'm still concerned about how deep the casting imperfection goes. Is there a way to be certain it won't be a problem ? Brazing , etc. Will the epoxy hold up to a possible coolant leak? Maybe I'm just perinoid but now is the time to make sure.

If you worried about leaks, take them to a competant local machine shop and have them pressure tested. It might not ba a bad idea to also have the combustion chamber and intake & exhaust runners cc'd to know how large you wound up making them with the grinding you did. You could also have a pair of ports flowed while in the shop to be able to validate the work you did.

You can only use the epoxy in the intake ports & as Blu said, have them pressure checked but I doubt you are going to find a problem.
Almost all the heads have some pretty good casting "uglies" (that's a very technical secret trade term :D ) in them.
Also, if you have a port flowed have them cc it also to see how big you may have made it just for reference.