Well, after a month of down time I finally got my ported lower Cobra intake back (thanks Tom Moss!). This time I put the right intake gaskets on - the gaskets I used when assembling the motor were .25" too tall for the ports but I was in a hurry so I used them.
I also upgraded to a 75mm MAF from the stock 50mm piece, and swapped out the stock 60mm throttle body for a 65mm Explorer unit. Swapped out the 19lb injectors for 30lb injectors while I was at it.
After working through a few bugs - bad throttle position sensor and an injector connector that had popped off - I got to rip on it a little last night. I was happy to see that it picked up a substantial amount of power. It feels 25% stronger!
The 331 was breathing through a straw with the stock 50mm MAF and 60mm TB. It feels great to have it back together and running to its potential finally!