Could I to cut corners for the time being run 2 of those pumps off just the A5 LT's one connector?
Nope... You can't draw 36W out of a single channel. Technically you should be able to draw 18W per channel, but I'd recommend using the headers in opposite sides of the row (1 and 4 for instance). The heatsink attached to the AE5 LT would be highly recommedable too (not sure if the AE5 LT ships with heatsink these days, mine didn't), and some air flow (not a dedicated fan per se, just make sure that the heatsink can actually dissipate heat, rather than being buried under a rat's nest of cables in some remote bay inside the case).
Does the PA2 come with the cable to connect the A5? (as I know the flow meter doesn't)
Not sure I follow... if you mean the Aquabus cable I don't believe so. However is just a 3 pin molex female-female cable (for the "low-speed Aquabus") and if my memory serves me well it comes with a "speed signal cable" (to connect the tacho output of the PA2 to a fan header in the MB for instance), I believe you could use that.
What's the best way to connect all the fans to the 1 header?
Personally I made some custom PCBs (very simple task really, 3 pin headers are easy to source, so is stripboard) because fan splitter cables are an unholy mess, and the available splitter PCBs at the time were of really poor quality. However if the soldering iron is not your thing, splitter cables will do.
EDIT: This pic may illustrate what I meant... It uses a different header to power the fans because it was more convenient for me, the 3 pin header is actually the power feed, but I think you'll get the general idea.