In the kits tab, use the "CLONE" option. Choose any team. Press "clone". The team list will appear. Choose the one that interests you. Choose kit number. Done. Now add yourself png or rx3 files and save the game.
You don't need to regenerate the game when you add a new kit. You have to regenerate when you edit one present in the game. If you create a clone and add png files for kit you need to save kit "floppy disk icon". Only then save the game.
I did your procedure but after saving the kit as you said, the shorts are yellow and the shirt is red but the minikit is the right one yellow shirt and yellow shorts because in your opinion I'm waiting for your answer from this problem many greetings.