Trek fiction is best enjoyed in general if you don't try to twist yourself into working it all into a single continuity. Can't be done, and trying to do so ruins the fun anyway. Hell, just the numbered TOS books would have taken about 100 years, give or take, to complete, and they only had 5, so instead of forcing it, just enjoy the stories.
The newer TNG/DS9/VOY era books work pretty tightly, but i'd bet you could even find issues there, and definitely don't always work with the old stuff.
It's ok, just have fun with the chracters. Continuity and canon just take the fun out of it