Weevil

Best answer as chosen by Asker / Ratings
The boss of Stone Temple (Twinrova?) shouldn't be a problem when using the Giant's Mask (this mask is found inside the dungeon). Just use your sword on it's tail and cut the pillars for magic jars.

Jirachi X

1st Bottle: This is the bottle you have now, the bottle you got of the witch.

2nd Bottle

Area: Goron Race Track (Snow Head Area)
Requirements: Goron Mask
Snow Head Temple Beaten
Powder Keg
The ability to race around at high speeds using the Goron Curl. Procedure: Make it Spring in the Snow Head area. Then go to the Twin Island area (in between Mountain Smithy area and Goron village) Don the Goron mask and roll up the slopes which normal Link is unable to climb. Then Blow up the rock near where the baby Goron is with a powder keg. The babay will then run inside. Once in, talk to him and he will tell you to race. Once you complete this race, you will get a bottle of Gold Dust (which can be used to upgrade the Razor Sword into a Guilded Sword)

3rd Bottle

Area: Romani Ranch

Requirements: Bow and Arrows
Powder Keg
Day 1

Be at the Romani Ranch at 2:30 AM on Day 1 and Aliens will show up. Fend them off with your bow and arrows until 5:30, if they get to the barn, you fail and have to start the 3 days over again. Once completed, Romani will give you a bottle of Milk. (Hint: The dog will bark at the closest alien to the barn. Also, beware the alien that comes from behind the house.)
4th Bottle

Requirements: Romani Mask
Knowlege of the Kafei/Anju quest in the bomber's notebook.

Procedure: Do the Kafei/Anju quest up until the Curiosity shop guy gives you the Letter for Mama. Next, wait until 10 PM on the final day, don the Romani Mask and enter the Milk Latte. Talk to Kafei's moma and give her the Express Mail to Mama. She will give you a bottle of Cheateu Romani.

5th Bottle

Waterfall Area (Great Bay)

Requirements: Zora Mask
Hook Shot
Ability to be a decent Zora Swimmer.

Procedure: Go to the Zora Domain area of the great bay and walk along the sand, past the Zora Jar game, and kep walking to you see a log. Once there, take out your hook shot and aim up until you see a ledg where you can see a tree. Hook shot up to it. Now you will see another tree... Keep hook shoting to the trees/chests until you se and entrance, go in.

Now, Don the Zora Mask and jump into the water where you see a Beaver swimming around. Z TARGET HIM! Unless you do this, he will completely ignore you. Once this is done, he will swim to the bottom. Follow him dowwn and talk to him. He will ask if you want to race for a bottle, say yes. To win the bottle, simply follow him through the rings and make it to the dam before the timer runs out. Once this is done, his big brother will appear and challenge you. Same concept, more rings. One completed, you will win an empty bottle. (Do this again for a piece of heart)

6th Bottle

Area: Graveyard (Ikana Canyon)

Requirements:
Captain's Hat
Day 3

Go to the grave yard on the night of the last day. Don the Captains Hat and tell the Stal Children to open up the grave. Once in the hole, tolk to the Grave Keeper and take him to the various sand pits (Z-Target and move slow, he has a short attention span and will lose track of you if you move to far away). Dig up three blue pillars of light and a Big Poe will appear. Defeat it and it will give you the final empty bottle.

About the boss, adding on from Weevil, if you do run out of green potion and all the ruins are ruined, you can pull out your bow and arrow and shoot the things in the tail (Not recomended unless you are positively are sure that you can not find any more magic potions... Or are a pro and want to challenge yourself).
To make this fight easier, you may also like to take in a few bottles of Green Potions, so if your magic meter runs out, you can just top it up again.

You could also find all the faries in the Snow Head temple and take them back to the great fairy and she will give you double your magic power bar.