The only thing that is directly answered by the rules is the cost.

PHB pg 112:

Wealth Other than Coins:
Trade Goods Table
1 lb of Tobacco costs 5 sp.

As far as effects, they don't directly exist for tobacco. You have already disregarded the main source (BoVD), and I would agree for 2 reasons.

1. Most civilizations don't make tobacco illegal
2. I've never smoked tobacco that potent that a saving throw would have been required to avoid negative effects.

However, if you want some mechanical impact and not just flavor, you could look at some of the weaker alcohols present in the game to see what kind of FDC you'd need to avoid "addiction". Again, tobacco addiction isn't the worst so even if you are forced 2 days without the worst thing to happen is you'll probably be a bit snippy with people (-1 or -2 on diplomacy cks?)

I like the feel you're going for for this character but I'd probably just stick to knowing the price and maybe going with what @Cow of Doom said as far as giving people a chance to notice hiding based on smell. (not guaranteed, but if they fail spot/listen maybe they can have a "Scent" check (Wis roll +1-+5 modifier depending on strength of tobacco smoked and last time it was smoked.) BTW, pipe tobacco does have a MUCH stronger scent than regular rolled tobacco.

Sidenote: possible "flavor" text, wiz/sor casting prestidigitation could alter the flavor of tobacco making it have a unique flavor!..the possibilities are endless, but it would definately increases the cost of tobacco if purchased that way. However, your party member could always burn a 0-lvl spell at the end of the day for you! (Side benefit for party members, it makes a nice aroma which is way more appealing that burning regular tobacco!)

I don't know of a canonical rules source for "here's how it works in D&D 3.5 when you have two characters in a single body," but I can point you to a couple of similar cases for which there are rules, from which you might draw some inspiration.

Schism

The psionic power Schism splits its user's mind in two, with each half able to take its own actions. While the source of the split mind for your character (presumably) wouldn't be the same, the description of Schism's effects sound a lot like what you're describing:

Your mind splits into two independent parts. Each part functions in complete autonomy, like two characters in one body. Your new “second mind” does not control your body physically but is free to take one standard action in each round if the action is purely mental (such as manifesting a power) in the same round you take your normal actions.

If your character concept concept is consistent with this setup, where one mind has control of the body and the other can only take mental actions, you could borrow from Schism's mechanics. Of course, since this option gives you additional actions per round, it would be a net increase in character power, so you might want to add some disadvantages to balance it out.

Fiend of Possession

The Fiend of Possession prestige class (Fiend Folio) has the ability to become incorporeal and possess characters and objects. Again, this is different from the fluff you have in mind for your character (where two characters are fused, rather than one forcibly possessing the other), but you can still borrow mechanics.

Again, this results in one of the minds being restricted to mental actions only:

While possessing an object, a fiend of possession can use any ability it has that requires no physical action, such as using a spell-like ability or telepathy. It cannot cast spells (since it can neither speak nor move), attack physically, or perform any other physical action, until it reaches a high enough level to make the possessed object perform these tasks for it.

Dvati

The Dvati (a race from the Dragon Compendium) are in some ways the opposite of your character concept (they're a single soul split into two bodies that counts as a single character), but you might want to reference them in terms of what kinds of actions might be restricted for action economy purposes.

For instance, when a Dvati character casts a spell, both halves are required to spend their action to do so (because doubling the number of spells a character can cast per round is ridiculously powerful), but they can move independently, each spending only their own action.