How do I check port alignment between intake and heads

I agree it is much better to mill the intake face of the heads but since the heads are already torqued then the intake needs to be milled. I would make a horizontle swath of dykem across the top and bottom of the head ports extended as far out on each end as you can then scribe a horizontle line with your pointer in the dykem on the top and bottom of the ports. Then do the same on the intake but in addition on the intake ends make an additional swath of dykem around the corners (8 swaths) with a scribed line turned around the corner so when you set the intake down (no bolts or torquing needed)you can see the scribed lines (it'll make better sense when you do it). level the intake side to side so the distance between the intake lines and the head lines is the same on each side & note that distance which is how far the intake needs to set further "down" in the "V". Your machine shop will do the math for the right amount to be milled taking into consideration the LA intake angles. As said remove the dowels & use "the right stuff" gasket sealer on thoroughly cleaned surfaces in lieu of the tailor made end seals unless the seals you have are the right thickness & most ain't as they are too thick. Do your mockup/measureing with the gaskets you intend to use (I'd suggest Felpro composition) #1243 for a 318. EDIT missed that you have a 340 which as you know would take a different number (couldn't find the FP number)