Mike,
Sorry I missed this one buddy! Tremendous effort so far! She does look great!
I would too agree on the weathering a bit. I can though out a couple of suggestions but please don't take these as a "this is how it should go" SBS bit.
I would give the whole boat a dull clear coat. Then apply a dark wash to the entire ship with burnt umber oils. This will bring out all the fine details.
Add some tiny chipping in key areas , especially where you have your rusting now. Anchor and anchor well, drainage ports, attachment point of the ladder rungs, hatchway handles and hinges, etc..... Use the tiniest brush you got or break a toothpick from one end pulling it back, creating a really tiny sliver point. Dip it in any dark rusty brown color.(like the burnt umber with a touch of Burnt Sienna). Just dab it into corners and ridges around these areas. Probably only leave a dot, pin tip size of paint when you apply it. This might take you a while, but will be worth it in the end. Where you might want to add some streaking of rust, follow up with a pin size dot of Burnt sienna. Let these dry for an hour or so (oils take forever to dry, so you have plenty of time). When you come back take a smooth flat brush, dip it in thinner, dab it into a paper towel a few time to remove all the thinner you basically just put on (solvents are still in the bristles) and in straight downward stroke pull the brush from you paint dots downward in the direction you think the rust will flow. You will have streaking. If too dark, dab out the brush and pull down some more...if you don't like, very lightly wet the brush with some thinner (not too much) and apply, take a cotton swab (bud) and remove it.
Typically subs rust above the scum line (there area where the vessel meets the water when it is just sitting there )
Seen here....
Picture for discussion purposes only
You can see the USS Ling has a small whitish line where the water meets the hull and pressure hull. SCUM. Salt deposits and algae. Depending on the service area of the sub, these can be almost non- existent and to brighter whites and greens. This can be simulated with oils too, just make the line following the "water line" of the boat using off whites. Don't worry about multiple lines, the vessel would certainly sit at different heights depending which point in it's tour it would be on.....less fuel, no torpedoes and such. A wash of lighter gray(s) below the water line would work nicely too. Salt water does a number on ships the second they hit the water. Not much rust would be on the hull, rust typically forms when the steel comes in contact with the open air.
My apologies for going on and on a bit. Hopefully a helpful opinion on adding some weathering.
I'll leave you with a great link to a USS Pampanito walk-around. You can zoom and rotate 360 degrees over the entire ship, inside and out.
http://www.maritime.org/tour/adeck.php?pano=nr
If your still on the weathering, try a couple spots and post-em! Would love to see you progress through it!
Good luck!! ;D