Just a suggestion, if you're planning to further work on the game and keep the main timer, then maybe you can pause the timer when player selects a tool, reads through the info for the mini-game and then clicks on a Start button to start the mini-game which continues the main timer. Then the results of the mini-game can be shown in the same mini-game popup and again main timer can be paused. Click on the OK button in the popup to close it and continue the main timer. You can additionally add or reduce time from the main timer depending on the results of the mini-game.