Manifold help
Actually the dowels are used for port alignment.
Turn the intake upside down. Take a straight edge and run it up the center of each port separator . Scribe a line around the top of the intake, Now you can physically see the center of the divider of the ports from the top looking down.
On the head itself the center is defined by the valve cover bolt. It is in the center of the port divider.
Set the intake on the engine with the dowels in place. Put the scribed lines in the center of the holes for the valve cover bolt holes . Now you just aligned your new intake to your heads. Tap down on the intake so the dowels leave a mark in the underside. Center punch them and drill them 1/4 to 3/8 deep. Now every time you install the intake you know for sure it is in the center of the port separators. Alot of guys take them out because they think they are for only holding the center of the end gaskets
Your intake probably don't fit. Meaning you are having a hard time getting the bolts started. Early heads pre 70 are different. Did any one try and put a 70 six pack on a x head motor. Now I am talking un cut heads or block. You probably will find it hard to get the bolts started also. A LD 340 intake will fit on a x head motor. Try and install a later intake and you will run into this problem. All later intakes are Machined for uncut 915 castings an newer with a 956 deck. All 340's with X / 894 heads were listed as 10.5-1 all later 340's with U,Z / 915 heads were 10.3-1. they didn't change the deck or the pistons in 70,71 it was the heads that were cut more in 69 back. This is the reason later intakes are tough to get on early motors. Today they make different thickness gaskets to help the installation,. And also its hard to find a block or heads that were not milled. Use this info however you want. Its what I found from building these motors for years. X heads were always known to be the head of choice. It was the increased compression that made them better . The castings were identical to the 915's it was the machining that made them perform better.