Why is "say" spelled differently for "said" and "says"?
From @FumbleFingers' comments to the question:
I don't think it's meaningful to suggest there's a "grammar rule" that led to the past tense of say being written as said rather than sayed, because we don't apply any such principle with, for example, bay, slay, pray etc. But I think it's interesting to note that when the verb “pay” means to slacken something like a line or rope, allowing it to run out a little at a time, the "regular verb" spelling may be validly used: He payed out the rope to give it some slack. - FumbleFingers
...you might find this discussion useful. I haven't read it in detail, but it appears to be saying that since there wasn't a time in the past where sayed was considered a natural choice, maybe it's not helpful to deconstruct the past tense as a version of say + -ed in the first place. - FumbleFingers
From the discussion in the second quote:
Our word sum analysis gives us evidence that <say> and <said> do NOT share a base, but the etymological evidence shows that they derived from the same Old English root secgan. - Pete, Real Spellers
Pete notes that saith predates says. He also distinguishes between a root and a base, and that while says and said share a root (secgan), they don't share a base (such as say, for example).
So the conclusion seems to be that said comes from saith while says comes from say.
The Bosworth-Toller Anglo-Saxon Dictionary is perfectly adequate to demonstrate that the Old English ancestor of the Modern English verb to say was a rather "strong verb" Wikipedia
Even if to say appears in Modern English to be a regular (weak) verb, it is not.
say, says, and said
There are different vowel sounds in say and said, making to say a strong verb.
While one might question the use of "i" and "y" to represent different sounds, there can be no question that say and said should be spelt with different vowels.
Much of Modern English spelling is a result of historic attempts to represent sounds . With printing and dictionaries, spelling became "fossilized" even while the sounds the spelling represented were still changing.
There are some spelling issues that general rules will not resolve.