Congrats on getting to this point - it's really not that bad once you get all the parts you need.
Some additional thoughts now that you are getting under way.
- use a thread chaser on all holes before you start - some of mine were not clean threads and I wish I would have done it before bolting anything together - I picked a set up at Summit and used it once I found a few issues
- anti-seize is also your friend during assembly as you will take it apart a few times to get everything lined up
- if you are restoring factory bolts - I would clean the thread on those as well to be safe
- you will want to install the 'cargo floor' step up piece before you put on the bedsides as you won't have access to install it once they are in place.
- I did need to bend/push/adjust my panels to get everything in to place - including expanding some existing holes (not visible) when panels are in place
- my gaps are not perfect yet - all parts open close/latch as they should with no binding/sticking (I'm driving the hell out of this thing just so I can enjoy it
Looks like a great start. Good luck!
*Added an 'after' picture of my project (same truck from my post above) for inspiration*
Can you share more details on your issue with the 'bed mount' pairs being too short?