This is not the usual, simple thing, Frege says about a and b though.
You seem to have assumed Frege is talking about a and b as signs, when he is not:
> If the sign "a" is distinguished from the sign "b" only as object (here, by means of its shape), not as sign (i.e., not by the manner in which it designates something), the cognitive value of a=a becomes essentially equal to that of a=b, provided a=b is true.
>not as sign (i.e., not by the manner in which it designates something)
Clearly, a and b here are the same in the "manner in which (they) designate something"
They even have the same cognitive value, not different cognitive values as with the example he started with wherein a and b did infact have different "modes of presentation".
Tackling your points directly:
>Frege is saying that the sentence "a = b" means that the names "a" and "b" are co-referential - that is, they refer to the same external object.. So the names "a" and "b" are not distinguishable based on their referents, but only based upon their shapes (or, their sound patterns when pronounced, etc.) and senses
>"a" and "b" are co-referential - that is, they refer to the same external object
>Quoting Frege: In that case the sentence a=b would no longer refer to the subject matter, but only to its mode of designation
There is no external object or subject matter referred to here there is only a "mode of designation" referred to. I believe Frege, making a mention of the many arbitrary signs one can use, has here used a and b as "arbitrarily producible events or objects" that are not "mediated by connection" to a "designated thing".
>and senses
I believe Frege in this example is tackling the very case of a and be being equated when they do not have different senses but are only different as objects, which I contend is not possible and that being a different object (be it due to the shape of the letter or pronunciation of the word) has to carry with it a different sense.
>Whether you write the name using Times New Roman or Arial is semantically irrelevant. The meaning of the name remains the same. Your use of the equality sign between font face inscriptions in order to create equivalence classes of letters is not the relation of Identity that Frege is discussing.
>If the sign "a" is distinguished from the sign "b" only as object (here, by means of its shape), not as sign (i.e., not by the manner in which it designates something), the cognitive value of a=a becomes essentially equal to that of a=b, provided a=b is true.
But he is, this is not the type of identity he got famous talking about, but it is the one he is talking about here.
The shape, as with the font, is what concerns him and his point seems to me akin to yours in that "the shape does not matter, they would both mean the same thing", in that for the 'a' and 'b' here, a = a has the same cognitive value as a = b (cont.)