I agree that you need to do the sleeve caps first. For most sweaters I've knitted, the side seams come last.
I also use a neat trick that really helps me with making sure my pieces line up properly once I have decided on the order in which I'll sew them up.
If you want the center of the sleeve cap to sit between the front and back piece it really helps to mark on each piece the quarter and halfway points. This is because there likely won't be an even number of stitches on both sides. For example, when you are working your mattress stitch you may sometimes have to go under two bars rather than one.If you have locking stitch markers on each piece that you have to match up, it will make these little decisions much easier.
It's really terrible to run out of sleeve cap to seam but you still have an inch of your front piece left. The markers make everything so much easier.
I can't remember my resource for this or I would link to it for you. I think it may have been an issue of Vogue Knitting or Interweave Knits.