I wouldn't bother port matching. It won't gain you any performance, and like you mentioned, no need to cut on a good factory intake. Most of the testing I've seen, and I think Jays testing always confirmed it, that a slight mismatch from a smaller intake port to a larger head port doesn't hurt anything, and sometimes is even beneficial.
The rear PCV should work fine. I typically don't even run one, but my stuff usually doesn't get short tripped, ran when it's high humidity, and never in the winter. The only time I had an issue was with my '68 Highboy in the winter time. Running one on the rear of the intake will work fine.