Don't touch the injection, std. deck height from GM factory/dart/whatever after market is 9.020 Most enginge builders deck them to 9.000 for "0" deck height on the pistons. We run 9.000 with Hilborn stacks on (5) 434" motors and 1 355" motor. You won't even see the difference in the deck height, we run .041 felpros and .060 cosmetics. We lay the intake gaskets on the intake runners and trim to fit the head ports, then transferr that to the hilborn and touch up the port runners to match if necessary. We do run both 3 1/2" and the 5 1/2" nozzles which put them into the cylinder heads with the fuel. What little air disturbance you'll get from mis-matched ports will be on the air flow and hardly noticable unless you're reaching for hundreths on ET. The injection units are machined for 9.000 deck heigth from Hilborn.
Now this is with std. 23* cylinder heads, i'm not speaking of special raised port heads that some manufacture's have they are an entirely different animal and have to be worked out.
JMO
Zip.