No...that's NOT what I"ve said
I know you have said the vent line should run vertically to the vent.
That's just the opposite of what I've said. The vent line needs to be as short, straight and HORIZONTAL as possible. Try to avoid a rise sharper than a 45 degree angle. So your vertical vent line that does a couple of twists and turns and is mostly vertical IS a problem, and so is the loop in it that's supposed to keep sea water out. Straighten out the vent line!
The exisiting hose seems to be one inch in outer diameter, when you say a one inch hose are you referring to Outer or Inner Diameter,
ALL hoses sizes are stated as the INNER diameter...all hose FITTINGS sizes are stated as the OUTER diameter. That makes it possible to know what size hose fits onto what size fitting.
If inner I will need to figure out if I can change the fitting on the tank.
You won't change that one...You'll put a threaded plug in it and you'll install a new vent fitting in the tank. That's actually pretty easy to do, thanks to a li'l gadget called the Uniseal
UNISEAL (Scroll through ALL the pages to see how to install and to get to the price list). A short piece of PVC pipe becomes a new hose fitting and it's done. Shields or Trident #148 is ok for head intake and tank vent lines. You'll also need a new vent thru-hull--NOT a "vent" thru-hull (they're only made in 5/8"), but an open bulkhead fitting
...the vent is just below the toe rail so assuming the boat is healed over it could be submerged at least some of the time.
Do you heel enough to put the thru-hull in the water now? If not, don't worry about it. If you do, it's an easy problem to solve: put a clamshell cover over the thru-hull.
the line from the Y valve to the through-hull is not continuous, it has a coupling where it passes through a bulkhead and then it also has a section under the sink that appears to be a brass inverted U which is anchored to the top of the vanitity which is then connected by a flexible line back to the the through-hull. I assume this may also serve the function of raising the line above the waterline.
That "brass inverted U" is actually a BRONZE vented loop (anti-siphon device) that's problly been neglected for so long that the air valve in it ceased to function a couple of decades ago. It's also installed too low in the boat to be of any value even if it did still work....vented loops need to be at least 6-8" above waterline AT ANY ANGLE OF HEEL--which means it has to be that far above the waterline not only when the boat is at rest but if/when the rails are in the water...which on most sailboats would put it 2-3 FEET above the bowl.
However, that's really all moot because you can't legally dump a tank in the Bay, so you don't need a vented loop OR a y-valve or an overboard discharge pump either in the tank discharge line. If/when you ever get the boat into any shape to do any blue water cruising where you'd be able dump a tank or flush directly overboard, it's a simple matter to install 'em then. It makes no sense to install anything you can't use now because lack of use is more damaging to equipment than constant heavy use.
But you WILL need a vented loop in the head intake...it does NOT go between the thru-hull and pump, but has to go between the pump and the bowl. See the drawing in the installation instructions for your new toilet.