Spiderman 1 with Tobey Maguire tells the story of how Peter Parker acquired his abilities.
Most of the time he is fully clothed. However, we are privy to at least one scene (the day he gets bit) where we see a super-skinny, ailing Peter Park about to turn into the Webcrawler.
We see a little bit of biceps here, but his chest is flat and he almost looks anorexic.
The next day, we see the new, improved muscular Peter Parker:
In real life, we know there was a lot of diet and exercise that came with this transformation.
My question is this: Did they film skinny Tobey first, let him bulk up and then film the rest of the movie? If so, how long can a movie studio wait while its primary actor works on his character? (e.g. in this case, gets ripped).
Actually actors are supposed to do such things, like losing or getting weight to fit to the movie part. Tobey Maguire did this more than once. Here's the http://en.wikipedia.org/wiki/Tobey_Maguire#Personal_life part:
Maguire has been a vegetarian since 1992 and in 2009 became a vegan. He often makes changes in his diet to either gain or lose weight for movie roles; for example, he dramatically decreased his calorie intake for Seabiscuit followed by a rapid increase to regain weight for Spider-Man 2.
In the first Spider-Man movie as you said Peter Parker was a nerd student; so it wouldn't be realistic if that kind of student appeared with those muscles. So he had to workout a lot.
This http://culture.com/articles/540/spider-man-interview-with-tobey-maguire.phtml says that:
Maguire spent six months taking martial arts, weight training, and an intensive gymnastics programme in order to bulk up, look buff, and be able to match the lithe athleticism of Spider Man.
Maguire worked out a lot to get into that condition. On the DVD commentary, Raimi states that one of the first scenes shot was where Tobey takes off his shirt and is not in great shape while one of the last ones shot was the one in the mirror you are referring to.
In this http://www.trainbodyandmind.com/2011/02/tobey-maguire-%E2%80%93-the-spiderman-workout/ you can read exactly all the exercises he did. This is the diet:
Diet – Diet was an important part of the program. All fried nutrition was excluded to make way for healthy fruit like fruit, vegetables, whole grains, fresh meat low-fat milk and cottage cheese. Tobey drank about one gallon of water per day (3,7 liters) and eat every three hours.
I don't know how they handled it in this specific case, but keep in mind that usually scenes are not filmed in the chronological order they will end up in the movie. Reasons for this are mostly logistical and economical.
If you have several scenes in the same location throughout the movie, it is just practical to shoot them all at once. Also factors like weather, rent for equipment and locations, actor availability etc are relevant to this.
So while waiting for Maguire to "bulk up", they could easily shoot scenes that appear later in the movie where he either does not appear at all or where his body strength would not be visible because he is wearing clothes. Stopping the whole production for this seems unlikely.