As has already been mentioned, don't rely on dry fitting for your measurements. It is difficult to get a dry pipe inserted as far as it will go once glued.
Best practice is to go one fitting and pipe section at a time. Measure - glue - measure - glue...
If you fit everything up dry and it expect it all to fit back up the same way after you take it apart and glue it, you will likely be disappointed.
Also, definitely use primer, and definitely use clear. It may be hard to find at HD, but plumbing or irrigation supply stores should have it, they will also have a much better selection of pipes and fittings.