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It sounds like you got tomato wilt. There are several diseases that will cause this general condition and they all look very similar to each other. All of them have no cure and you cannot plant any tomatoes or nightshade plants in that location for at least a year (2 if possible) as the disease will stay in the soil and attack any nightshade plants planted there. This article has all the different types of wilt that can attack tomatoes:
https://www.gardeningknowhow.com/edible/vegetables/tomato/wilting-tomato-plants.htm

Here is an article that you may find helpful: https://www.gardeningknowhow.com/ornamental/flowers/gardenia/helping-a-gardenia-bush-with-yellow-leaves.htm

As for pruning the gardenia, you may want to hold off on anything too drastic until its normal pruning time in summer. This article will help you with that: https://www.gardeningknowhow.com/ornamental/flowers/gardenia/when-to-prune-a-gardenia.htm

This article can provide some suggestions: https://www.gardeningknowhow.com/ornamental/shrubs/shgen/shade-loving-shrubs.htm

Care for them as you would a houseplant until the leaves have yellowed and dies back. Make sure to place them in bright light and water when the top of the soil is dry to the touch. Once the leaves die back, place the plant in a dark dry place. Then, when you are ready to plant the bulbs, remove them from the soil and plant them outside.

Taking the flowers off forces the plant to focus more on the roots, which is what you want to harvest, instead of flowers and then seeds. So it is helpful to prune the flowers.

Yes, they need at least 7-8 weeks of temps below 45 to bloom the following year. Refrigerate them both for at least this long, or preferably 10-12 weeks.