i have done some research for the problem with skills and it seem that you could get more than 2000 but only if you manually change the json file that contain the table with the skill i don't really know how it work i just wanted to help so for more information here the link of the forum where i find the information
https://forums.rpgmakerweb.com/index.php?threads/increasing-database-limits-pote...
if it don't work i not sure if each level of a skill is a seperate skill in the database if yes maybe just reduce the level max to some skill to 20 or 15 so it save some place but i don't know how it really work sorry to not be able to help more