Try Total Baseball. My copies have details of the rules from 1876 onwards. The Genesee County Rules that were linked to are not the authoritative version of 19th century baseball rules, nor are they comprehensive (or even complete in the linked version), since the rules changed several times in that century.
I will also point out that some of the things you think I got wrong are repeated in the linked document. For example:
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For an online list of all the various iterations of the baseball rules, try here:
http://baseball-almanac.com/rulechng.shtml.
Check, for example, the 1867 entry, making the pitcher's box a 6 foot square, and giving the batter the right to call for a high or low pitch. In 1879, a base on balls took 9 balls, which was reduced to 8 in 1880, reduced to 6 in 1884, 5 in 1887, and finally four in 1889. In 1887 it took four strikes for a batter to be out. From 1863 to 1867, a pitcher was not permitted to move his feet when pitching. It wasn't until 1883 that a pitcher was allowed to deliver a pitch with a throw from above his waist.