My block was zero decked. The intake fits perfectly onto the gasket in relation to the heads, but it doesn't seem to low enough. I'm thinking this might be the problem? Would an okay remedy be to put a bit more silicon sealer on the end rails to make the gasket? I would think that would be alright but just wanted to check. Thanks.

I think you're confused.... you have something backwards.

Decking the block would cause there to be TOO LITTLE gap between the intake and the block, if it caused the gap to change noticeably at all. If you deck the block and then deck the heads too A WHOLE BUNCH, the intake surface on the heads moves inward and down, and the intake won't fit far enough down between the heads for the bolt holes to line up. But then if you cut the intake narrower so that the intake can fit down in there far enough for the bolts to line up, the bottom of it will be too close to the block, so you have to cut that place on the intake too. Most likely though, if the intake fits between the heads and the bolts will go in it, it's fine.

So, there's probably not "too much gap"; just go ahead and use however much silicone it wants you to use. Personally I prefer to use nothing but silicone (no rubber gasket), others may prefer otherwise.