Hello RX, can you put a level on top of the tracks, if it's a small level then find something long enough on top, then the level on top of that, see what it tells you.
The other problem could be a dirty track or the wheels are damaged, love to see it.
One way to fix a jumpy floor is to cut a square in the floor next to where the problem is, then take the floor away, then you can find the stump causing the trouble, then there are a couple of ways to fix this.
If the stump has worn away, then you can replace this stump with a concrete stump, they are cheap and concrete it in, using 'rapid set' or 'quick dry concrete', attach the loop on the stump to a bearer, give it a day to fully dry, although a few hours could dry it, then replace the flooring.
If the flooring has dipped down then you may want to jack it up and pack it, again love to see it.
Well done RX on the canoe, I'm sure it looks fantastic.