I know the shafts are just laid in there for now and you will have them adjusted and secured when you get them inplace. Use a leveler Paul and lay it across the tubes so that it will show them level across from each other. Gears will work just fine for your model.
Checked the level last night and made some adjustments last night. No matter what i do I am about a 1/4 bubble off. The upside is that I am a bit closer to the rudder. So I think I am happy.
Looking at this angle I would say you want the props closer to the hull of the ship. I have to take pictures tonight, I'll get one of my Arizona props. It looks like the sides curve up which means the props can go up. This will be achieved by cutting the supports down a bit.
The cut on the stbd side will allow the shaft to drop lower inside the hull. I think the port shaft I didn't get a chance to enlarge to the same dimensions as the port side. When I had the shafts tacked in I had the tubes much closer to the hull. I am pretty sure Paul you should be able to install your motor mounts to the hull bottom level with the tubes. I was testing with the BC geared motor mount . Get the rudder in Place Paul and make adjustments till you get it line up. Keep the pics coming after each adjustment so that we can guide you.
If you have settled on the prop size you are going to use, then I would try to get the props as close to the hull and the center keel as possible. My Richelieu's props are within a 1/16" of the hull. It helps prevent water from spilling off the prop edges and possibly reducing thrust.
I am running a pair of 1.25 inch props. I don't foresee myself wanting any larger props on this boat. Direct drive and drag props should get me down to 26 seconds.
I never noticed how lumpy the bottom of the zona was. I am getting set to redo the whole ship again. She is loosing the gears, getting bilge keels, different gun placements and a nice "detailed" makeover. I figure I am not battling her so I have time to experiment with different things and add details. The ship has a lot of cool things to model. I have to make her look like she is from the 30's
Well Have cut down the struts to get it closer to the hull but now I have run into a problem. When I check where the shaft fits into the hull it is sitting on the bottom. The shaft itself is touching bottom.. It is really only impacting one shaft. The other is at motor hight if the motor is placed on the bottom of the hull.
Don't worry, you probably have to cut the hull holes a bit longer. Mount the rudder, make up motor mount blocks and mock up the dog bones and brass collars. Don't mount the motors on the bottom of the ship. You want them sitting out of the water in the water channel. If you keep them in water, you will wear your motors out faster and loose speed half way through the battle when they are wet. You will also burn the brushes out quicker.
Before yo make the mounts Paul I'm sending you this link and another link. The phots of the interiors and equipment layout will help. Here's the first link to this site. Go to Members and you can click the members ships and see how the ship was built. Excellent references. http://www.mwci.org/chapters/TNB/CTBG/members.html