Already tried this a few days ago and its not correct. I tried a black bear with reload x2 accuracy x2 speed x2 replenish melee attack. Couldnt get the range upgrade.OK I had 10 rank 9 vets who had no upgrade points spent, just regular units with a lot of experience that I prefer to use as regular units to save money. So, I did some testing. I'm 99% sure the below is correct.
The problem is when you take a clan token skill that you already have regular skills spent on, it seems the regular skills grey out and don't count anymore. So if you have 2 regular accuracy, 2 regular reload, and spend 10 tokens on the 3rd advanced reload skill, the game sees you as having spent 3 skills because the top 2 reloads are greyed out. Thus, this unit will never have the prerequisite 8 skill points spent.
Melee attack and increased ammunition all work okay on line infantry because there aren't free 50 koku upgrades on those up top for line infantry which could cancel the above. They're all 70 koku at the bottom with 10 tokens. Note however some units have melee attack both up top and on the bottom. An example is a shogunate guard cavalry unit. If you have 2 melee attack up top, 1 or 2 on bottom, you can't get a rank 9 skill (Banzai or inspire).
Just to confirm my tests and prove it's not just reload and accuracy causing problems... I wasted 10 tokens doing something dumb on purpose. I made a unit take 2 speed and 2 reload, then spent 10 clan tokens on a 3rd speed down below. Then I upgraded it with junk up top (fatigue resists, etc) until it was rank 9 time. I could not get any rank 9 skills on this super fast unit. Then I deleted the unit.
With that said, discussing how to upgrade units might be useful. For example, on my line I obviously want 2 reload, 2 range, increased ammo, and long range. That leaves me 3 skill points to spend on random stuff. I ended up putting them in speed, melee defense, and melee attack, figuring they might melee cavalry by accident sometimes.
What would you do with those remaining 3 skill points? Is fatigue resists better than speed? Is a 2nd speed better than melee attack upgrades?
For rifles... after your obvious no brainer 3 accuracy and 2 reload (and eventually 1 range) what do you do? Speed? Enemy spotting?
Hope this helps.