I believe you can only get the upgrade materials up to level 35 with crystals. Anything beyond that requires money. This is my guess based on how this has gone so far: it is probably only a good idea to purchase the level 35 and below materials for the first character in the cycle of six, so in this case, just for Luke. I can't absolutely confirm this, but I believe each successive character, in the first round of their marquee, gives you enough material to upgrade, not to the current level of your lowest character, but the level that is nearest to the level that is evenly divisible by five of the lowest character. In other words, if you had all three at say level 49, you would be able to take assaj to 45, if you bumped each one up a level, then you could take her to 50. That is just a current theory based on what I observed with Yoda. I didn't pay enough attention to IG when I leveled him.
As for progression, when you get to these ability levels (the ones evenly divisible by five), you always need some extra material, and that is what is in the 40 and 90% boxes. Eventually, you hit a point that you need a new type of material, and that is what is in the 100% box. I'm close to where you are, I have everyone at 49. Once I get some more Mk V, I can take 2 to 50. I just got Jotaz to tier 5. All other enemies are still at tier 4. At this point, I know I have to get 100% on the next ones to get more Mk V. Once I get everyone to level 55, then I will need to beat tier 5 in order to get the next batch of material to advance.
Unfortunately, it seems these runs can be quite random. I think there is a good deal of rng involved on whether you dodge certain attacks or get crits on your attacks. Sometimes I get a great run and get several boxes and then, even after making upgrades, go back in and do 25% less that what I just accomplished. I think there is a learning curve involved at this point.
Overall, I think besides buying the currency, which I don't think we get enough of to advance at this point, your best bet is to buy the level 35 and below stuff on the first toon only and buy it day one so that you get higher in the coliseum as quickly as possible. My rank has been pretty steady except the past few days where I have finally seemed to advance. I think some people might have given up or I have just got some lucky runs that allowed me to upgrade more quickly. The higher the level of the initial toon, means the higher level of the next one added.