chris forbis I think has been messing around with some gaining whilst unable to do much lower body work due to a back problem. Hopefully he can add some wisdom here.
definitely a lack of squatting and deadlifting will limit somewhat the growth stimulous, although it certainly won't prevent it entirely. I would suggest adding lower body weight bearing as soon as possible (e.g. farmers walks or even just standing supports) just to keep downstairs tough.
as far as keeping lean while gaining, i see 3 basic components: genetics, food quality/timing, and rate of gain. we all know at least one person who eats like shit, doesn't do shit, and looks like the incredible hulk (sans green tint)--genetics will definitely play a role in how lean you stay. judging from what little i've seen of you, i imagine you'll fair pretty well in this regard. food quality you understand of course--really getting control over insulin, etc. finally, how quickly you attempt to gain a given amount of weight will play a role. a lot of times the attempt to gain will outpace the physical ability to gain, consequently resulting in some fat gain. in other words, if your body can only stick X calories into muscle building per week and you're eating 2X calories, you're going to get soft. the trick of course is finding what X is, which is next to impossible, particularly with day to day disparity in activity, sleep, stress, etc.
no idea if that answered any of your questions.
also, titanium body parts are sweet.