Seems like you already know the answer on the lube question, there isn't supposed to be gear oil in the knuckles.
As far as the inner axle seals that were "too small" in the axle rebuild kit we sold you, I would love to see them, could you please send them too me, I will cover the shipping & your time. We have sold & installed literally thousands of these kits and I have never had a complaint about inner axle seal's being to small... Not saying it hasn't happened, just saying I am yet to hear of it.
It is possible that FJ40 vintage seals were put into the kit by mistake (they are not assembled by us, however I will start checking the components prior to shipping.
A couple other things that may come into account...
1. Most generic 4x4 guys are NOT familiar with the Toyota knuckle design, especially in regards to inner axle seals, lube, and gear oil. I have seen them delete the inner axle seal (as they beleived it wasn't needed) and let the knuckle be full of the same gear lube as the axle... All under the pretense that "older closed knuckle axles did it".
2. I have seen people "miss" the inner axle seal completely. I have had a handgul of calls stating "where does this little round seal go?". Usually because they have not completely cleaned the grease out of the ball, thus allowing the seal to be seen.
3. There are those that choose to NOT replace the inner axle seal not because they didn't see it, but because the thought it looked OK, didn't have the tools to do the removal (easy to fix

), or they had bought a wiper seal kit thinking they were doing a knuckle rebuild.
4. The seal can easily be damaged by improper install techniques... if you are rebuilding your knuckles for the 1st time... do yourself a favor and buy an extra inner axle seal (hell, ask me nicely when you order and I will toss one in if I have loose ones...

)
Hope you get it all sorted out, and let me know on those seals... I would love to get that figured out before it happends twice...