You're trying to create a floating Chernobyl!
First let's talk about the vented loops--you'll need one in the toilet intake and one in the line to the seacock. BOTH should be at least 6-8" above waterline AT ANY ANGLE OF HEEL, not just at rest...which, on most sailboats, puts 'em 2-3 FEET above the toilet. The intake vented loop needs to be installed between the pump and the bowl...if you put it in the line between the thru-hull and the pump, it'll prevent the pump from priming. Knowing all this, is that cabinet still the place to put 'em?
I'd return the Jabsco
y-valve and exchange it for a Whale. Reason: Good y-valves have a "barrel" inside that the handle rotates to line up with the holes...the Jabsco has only a flimsy little "gate" that the handle swings from side to side to block/unblock the flow. Even a grape seed can jam it...and I've never seen one that's more than a couple years old that doesn't leak. The Whale is the same price
or less and is top quality. Drill a hole in the handle to run a tie wrap through it.
Now...about your proposed plumbing
Coming out of the toilet, go to a y-valve--the ONLY y-valve in the system...one side to the tank, the other side to a vented loop and then the thru-hull.
Instead of a y-valve in the TANK discharge line, we're gonna install a second fitting (I'd pump out and THOROUGHLY flush out the tank before doing this)...it's actually easy to do, thanks to a li'l doodad called the Uniseal UNISEAL
(scroll through ALL the pages to see how it works and to get to the prices, which are dirt cheap). A piece of pvc pipe and you have a new fitting.
You're gonna run the second line to a tee in the toilet discharge line installed just before the vented loop.
However, there's one li'l detail you've overlooked: unless the entire tank is above the waterline, you're gonna need a pump--either a macerator pump or a manual diaphragm
pump--to dump it. We need to figure out where to put it.
That accomplishes everything you want to do cleanly and simply.