Any time you work on a bike there is a chance of messing it up.
Can't help much with the BB- sealed bearings? If so then they might just be a bit sticky from storage, could heat up up with a torch(if there are no plastic dust covers on the BB or Bearings) for a second to see if that helps. If the BB went in nicely without too much trouble you probably didn't cross thread it. Might put some grease on the spindle too.
For the headset- I assume you have a headset press? Just make sure you have the race and cup on the correct side of the headtube. If there are logos you would like to show make sure you line those up too. You should use some light lube to help you along(and help prevent any chemical welding between aluminum parts) Just take it slowly and be sure that everything is going in smoothly and evenly and you will be ok. Don't overtighten the press on the frame, you are more likely to damage the headset cup than you are the frame. Once the cup and race are properly seated all the way in don't tighten it any more.- for cheaper frames I've used a makeshift press-dont recommend it for a nice build tho.
For the fork race I use a piece of pvc pipe just wide enough to fit around the steer tube and a couple inches longer than the steer tube. Put the race on and again use a little light lube. Put the fork on something that will cushion the dropouts(like carpet) and make sure your fork blades are properly supported(dont want them to break). Use a rubber mallet to tap the race onto the crown. Sometimes this takes some considerable hitting. Just be very careful with your fork blades(dont bend or crack em.)
Just take it slow and make sure everything is going on evenly and you will be fine.