From what I can tell, in order to get an EX File key from Gardening you need to max out breeding on all the items. This is fine for heal berries but how are you gonna get about 100 small flowers?

I´m sorry, but I don´t really see the problem here. Wouldn´t u just keep on breeding, harvesting etc etc, till u have enough? (and it would be 99 I presume )
It might take a while tho.

I did it I did it!!! The reason why, I forgot to turn my system off at night and I forgot all about it... See no worries there!

Small Flowers are extremely diffcult to grow since they have a low chance of being grown, until you improve it's growth rate through harvest. The best way to get Small Flowers or other item you're trying to max out is to use all seven flower bed for that item, then continue the game.

Battle make time pass by more faster than not battling and allow items to grow in the garden. You could leave your PS2 on since item still grow as time goes by. Just keep improving the breed process, so you have a better chance of obtain the item. All item must have a breed rate of 100%, so have fun with that.

it's just a matter of time and luck since Small Flower start at 5% chance of growing until you improve it's breeding rate. There's not a large number of Small Flowers in the game, so if you can, use them to improve the Small Flower's growth rate.

Also, I have a slightly quicker way to make them grow. Go to Baskar and stand to the left of the bed that is seperate from the others. Hold the analogue stick to the right (which should make you walk toward the bed if you adjust the camera right). Then repeatedly press X and hold the stick and you will just repeatedly go to sleep. Turn the TV off of Auxillary and watch a show while you do it. This is good, as sleeping at an inn is one of the things that passes time for the flowers to grow fastest.