If the header flanges cover the holes you can just shove some pieces of 1/8" steel welding rod with high-temp silicone in them. I did that for the 360 in my D200 because I replaced the heads with rebuilt late-70s ones I got from a member here and I was lazy lol, it's been holding up for a couple years now though with no signs of leaking. Tapping and plugging is better though for sure.
I'd also put a TF-2 shift kit in the 904/999 for some insurance that it'll hold up to any power upgrades down the road and to make it a little more fun to drive.