With three exceptions, every line on one set of pages begins with the word "Let" and every line on the other pages begins with the word "For."
In 1950, W. H. Bond noted that some of the surviving "For" pages were dated to match some surviving "Let" pages, and that a sizable clump of "For" lines on those pages referred one-to-one to the corresponding "Let" lines. This indicated some rigorous ordering on Smart's part -- probably by following a procedure of writing one "Let" line on one page and then writing one "For" line on the other.
Assuming a call-and-response pattern, Bond in his subsequent edition of 1954 printed those "Let" and "For" lines as couplets rather than on separate pages. In her 1980 edition, Karina Williamson followed suit.
Smart's intentions while writing the manuscript are unknowable, and the manuscript remained unpublished during his lifetime. But he did not write couplets in manuscript, as he easily might have, and the call-and-response pattern is unarguable only in lines 1-158 of the "Fragment B" manuscripts. In lines 159-295 of the "B Fragment" pages and lines 1-162 of the "C Fragment" pages, continuity within pages is much stronger than the continuity between pages, and so there seems little reason to assume a couplet format.
That's about a two-to-one ratio between unlikely couplets and probable couplets, and so it seems safest to me to print the sequences in separate units, as Smart wrote them. I've therefore placed the dates for which both "Let" and "For" pages survive into frames, with the "Let" page in one frame and the "For" page in the other. Clicking on the first word of the line in one page will position the parallel line of the other page to the top of its frame. My hope is that this will allow some primitive synchronization while preserving Smart's original format.
With similar conservatism, I've discarded editorial corrections, no matter how intelligent, in favor of the manuscript reading whenever there seemed to me to be any possibility of ambiguity.
This is a manuscript (probably first draft), and so readers need to work a bit to give it the benefit of the doubt. The best way to gain that benefit is to track down a copy of Williamson's Oxford edition and its downright heroic set of footnotes.
It's a very expensive benefit, however: both the Bond and the Williamson editions are long out of print in the USA. To my knowledge, despite its importance to twentieth century writers and readers, the complete manuscript of Jublilate Agno has never been made available in paperback form.* For lack of any other form of distribution, generations of teachers and poets have photocopied it. Which is why I've put it on the web.
* Reader A. B. Jackson informs me that Penguin Classics published in 1990 a paperback Selected Poems, edited by Marcus Walsh and Karina Williamson, which includes the complete Jubilate Agno. Jackson calls it an "excellent collection," which I easily believe, given Williamson's participation. I haven't found the volume myself -- it must have come into and gone out of print during a window of inattention -- but used copies might turn up, and one can always hope for a new printing. There's thus less pressing need for this online affair and greater likelihood that I'll remove it at some point. If it takes your fancy, I recommend you make a copy.