It's actually pretty simple. You can attack flaws and specifics within the texts and practices of a religion, but ultimately an individuals faith is his or her own

I agree and this was exactly be my argument against him, religions as a whole and in general can have flaws, and you can point them out. It is important to understand their being different interpretations, however you can still point out flaws in certain religions. It is relevant, because the pros and cons of a religion as a whole will effect the individual.

If you attack a specific passage that that individual happens to see as a metaphor, you pretty much don't have anything to attack insofar as that individual is concerned. If you do the same to a religious individual who concedes that there may be inaccuracies in the text due to oral tradition, translation and re-translation, again you pretty much don't have anything to attack insofar as that individual is concerned.

Then im pointing out flaws of a religion that may or may not apply to the next person whom believes in it. I don't see why I can't do that.

Attacking the general flaws of religious texts is pretty much pointless because of that- it MIGHT be useful in the odd case of the individual believer who considers the entirety of the writings to be both literal and infallible, but those individuals tend to be particularly inflexible in their beliefs and fairly close minded to facts even if placed right in front of them.

I agree however, if we completely stop criticising these beliefs however then no progress will be made and the ignorant and closeminded will never deteriorate over time.

Yeah, I mean, you might not like what NAMBLA stands for, but saying anything about it is pointless as the viewpoints of individual members are their own (maybe they just go to the meetings for the potluck).