Oh my...so many questions!
And some you didn't ask...I would not put any money into a Jabsco toilet. The service kit costs almost as much as a brand new one. Jabsco toilets are so flimsily built that you'll be lucky to get two trouble-free years out of a new one. So as long as you're replacing everything else in the sanitation system, replace the toilet too...with a decent quality one. The Raritan PH II will only cost you about $125 more than a service kit for the Jabsco, and has been rated the best manual toilet under $500 for decades.Check the Ronco Plastics catalog before ordering a tank...they make TOP quality tanks for a very reasonable price...they sell direct...and have more than 400 shapes and sizes, over 100 of which are non-rectangular. http://www.ronco-plastics.comWhere are you planning to put the tank? Depending upon where the head is located, there may be a better place. (1) Do you recommend installing a clean-out on top of the tank or do they leak odor over time?I would install a cleanout. The rubber o-ring under the cap ceates a seal that won't leak.(2) Instead of running the discharge line out of the side near the bottom of the tank as it was previously, I intend to run it from the side near the top with a elbowed tube running to the bottom of the tank on the inside (is thisadvisable and if so, how far from the bottom should I be with the interior tube)? Not the best idea, 'cuz the pickup tube is actually attached to the fitting, not the tank. Last I heard, Ronco (who makes Raritan tanks, btw) doesn't do it...on the top, or out the bottom only. So you'll have to make the pickup tube yourself. It should touch the bottom of the tank, cut at a 25-30 degree angle.(3) I would like to have all of the outlets run from one side (1 1/2" inlet, 1 1/2" outlet, 1" vent), as it would require the shortest runs for the tubing and also put the vent outlet at the highest possible point in the center of the tank least subject to heel. Is this OK or are there disadvantages to this arrangement? It doesn't matter where you put the discharge fitting...the inlet and vent fittings should be inboard on the tank, on or toward the boat's centerline.(4) Per your recommendation, I am stepping the vent line up to 1" since it will require one bend and will rise for several feet above the tank.If it has to rise several feet AND will have a bend in it, we need to find a better location for the tank. Is there any type of thru-hull vent fitting you recommend?Open bulkhead fitting, with a clamshell cover over it.(5) Lastly, the head and tank are below waterline and with my planned arrangement will have fairly short runs. Is a vented loop required? At least TWO vented loops are needed--one in the toilet intake (between the pump and the bowl, to replace the short piece of hose the mfr uses as shown in the illustrations in the installation instructions for your toilet)....another in any head or tank discharge line connected to a below-waterline thru-hull. None is needed in a line going directly to the tank if the inlet fitting is inboard on the tank. You didn't ask about hoses...the most odor-permeation resistant sanitation hose on the planet--proven in independent testing to be at least 16x more resistant than any other hose--is AVS96 http://www.aussieglobe.com/avs96.htm Only available direct from the mfr...$5.50/ft. It's only available in 1.5"...use Shields or Trident #148 for other sizes.As for your residual odor: buy some Raritan K.O. holding tank treatment...it's a live bacteria product that "eats" odor-causing bacteria and spoors. Put it in a pump-up garden spray bottle...spray every inch of every nook and cranny in every area you have odor, including any carpeting. Do NOT rinse...leave all hatches and lockers open for at least 24 hours so that plenty of fresh air can circulate...turn on fans if you can. Remove the covers from your cushions...spray both sides of the foam enough to make sure the K.O. penetrates all the way into the middle...put 'em out in the sun to dry for a day. If your covers aren't also dirty, you can save yourself a cleaning bill...spray them andleave 'em out the sun all day.Btw...this also gets rid of the musty odors in wet lockers, foulies, PFDs etc. I think we should prob'ly talk a bit about the specifics of your tank installation...send me an email (I'm in all the owner directories) and I'll be glad to help you sort it out.You might also check out the link below.