Bruce,
Thanks for those references. That is very interesting that the one reference states the gage is four feet. But there seems no doubt that the actual gage of the railroad after correcting the mistake was 4’-1”. However, even though the source cites the gage mistakenly as four feet, it does indirectly add some degree of evidence that the actual intended gage was four feet rather than some larger number that would be required by Mr. Agassiz’s explanation. Mr. Agassiz does indicate that he was not thinking clearly when he wrote the letter of explanation.
I almost think that the very confusion that led to some sort of acknowledged gage mistake has persisted and affected the very explanation of that gage mistake.
The biggest mystery I see is how you can build thousands of feet of railroad without knowing the gage.