For my 460 build, I ended up making my own gaskets based on the alignment/position of the installed intake and was able to successfully address this issue.
I started by making 8 alignment bushings (4 on each side) and dropped the intake on w/o gaskets with alignment bushings and bolts finger tight. I leveled the intake from side to side with a stack of feeler gauges and then measure the intake to head clearance (gasket space) on each side of the intake. I ended up with 2 different gasket thicknesses (1/64 and 1/32).
For you, if you can't get the bolts centered w/ no gasket, then you have no choice but to machine the intake to take material off to lower the intake down. You would have to measure or estimate the amount off-centerness and then do the trig to calc the amt of machining. The idea of opening the holes in the intake might address the installation ... but it can't be good for your port match.
On my build, I used felpro gasket material/paper. Both gaskets are thin, but the gaskets have some crush in them after torqueing and I believe they are sealed. The intake (Victor 460) is brand new, so I have a good surface to seal against. The clearance was pretty uniform vertically up the sealing face and front to rear. Just different on each side. Another solution was to machine the intake, but I didn't want to go to the trouble this go-around. At some point, I will cut one side of the intake to make the gasket thickness uniform at 1/32. Note on the front and rear sealing surfaces, red RTV was used. I never use the end seals.
I will start the engine in about 6 wks to know for sure if it is sealed, however I have made my own intake gaskets in the past and they have worked fine. Just wanted to share that with you.
A side note ... that with the fore mentioned alignment bushing, I was able to use the gaskets as a templete to get a near perfect port match between the intake and head, installed on the engine. I can see 4 of the 8 assembled ports and the alignment looks awesome.
Process: I used the bushings on the intake and made the gasket with a perfect match. I then transferred the gasket and bushings over to the head ... and then blended on the heads to a perfect match to the gasket. I chose the head to blend cus I'm using a Victor 460 intake and DOVE-C heads and there is a huge port mismatch that needed to be addressed. It was a pain the make the bushings since I don't have a machine shop, but they worked out very well for my build.
In my opinion, you have a very narrow window to get a good port alignment between the intake & cylinder head. Hence, I think a custom gasket/alignment bushing approach is required or perfectly machined parts tailored to the gasket you are going to use. If +/- 0.100" mis-alignment is okay, then either approach is not necessary. But for me, I'm going for +/- 0.020" ... however it sure is a lot of work.
Sorry for the long rely. Good luck with your build. Cheers.