I'm sorry it's taking so long to help you out, but sometimes it's hard to decipher the real problem. I'm still not exactly seeing it, but I'll do my best here.
First of all, it's a bad idea to record guitar first. The drummer is the timing glue that holds the band together, and the entire group should be following him. It's going to be extremely hard for anybody to stay in time with a lone guitar player who's got the lead.
What I would recommend is one of the following:
1) Use a click track and make sure you've got the whole song scripted out (e.g. you all know where you come in). Have the drummer play to the click track, and perhaps have somebody else in the group play an instrument that the drummer can monitor through headphones (so he doesn't get lost). Once you have a drum track, you're golden. Now, you don't have to do drums first, but it helps with the changes. As long as you've got the click and everybody can follow it, you can do your tracking in any order. Typically drums and bass (the real rhythm) get tracked first both for timing and groove.
2) Have the whole band play record a "scratch track". That is, record the entire group play the song naturally, with or without a click track. This doesn't have to be a top notch recording. As long as it's predictable and the mood is right, you should be able to use it as a guide to start layering your good instrument & vocal tracks. It's a good idea that the scratch take be multitracked if possible so that you can cut various instruments in & out while tracking, but not necessary. At any rate, this can work well if the band is pretty tight and can reproduce its sound consistantly.
3) You can totally fake it and write your drum parts in fruity loops, then use the fake drums to track your instruments. Later, you can either have the drummer play to the drum track, or you can very easily convert the drum track to a click track and have him play to that (and the rest of the instruments you've tracked of course!).
Really you have to find what works best for you guys. Unless you're really special, however, you're going to have timing issues if you try to use a lone guitar or single player as a guide.
Now in regards to your lining up issue. When you record a track using another track as a guide, is the newly recorded track *physically* behind the guide track? You could have a lag issue and it would most likely be due to your soundcard. I've seen a few instances in the past where recorded tracks would be damn near a quarter of a second behind! It's pretty rare though. What kind of soundcard are we talking about?
Slackmaster 2000
