As long as the pushrods are the same length it's no problem. Just different styles of pushrods. And btw pushrod length makes no difference whatsoever on valve train geometry on a engine (such as a small block mopar) with a shaft rocker system. The shaft mounting height and valve stem height are all that can affect geometry. As far as the intake it appears that the Holley was setting too high thus the reason they hogged out the holes. Definetly not the right way to do it. Check to see if there are dowel or roll pins in the block on the front and rear China rails about half way between the heads. If so pull them out and see if the intake sets down farther. If so that may solve the issue. Also, if your using the cork gaskets on the china rails eliminate them and that can possibly let the intake set down farther and allow proper alignment. I always eliminate the cork gaskets anyway and use RTV and they generally seal up much better. If Neither of those methods work most likely the block and/or heads have been milled a bunch and if your already using thin (.040~.045") intake gaskets the only way to properly fix it is either pull the heads and have the intake surfaces milled down or have the intake itself milled down. My method for determining how much to mill is to set the intake on with no gaskets and use feeler gauges at all 4 corners between the heads and intake to determine how high the intake needs to sit so the holes are a little above center of the bolt holes in the heads. You want them a little above center cause when you tighten it down it'll pull the intake down