Q1: Is the card placed on top of my security stack by this card’s effect the Digimon played by my opponent or the card revealed from my hand?
The card revealed from your hand.
Q2: Can I activate this card's Opponent's Turn effect when BT9-103 Kongou's effect is preventing cards from being added to my security stack?
You can activate the effect, but you can't add cards to your security stack, therefore the revealed card can't be added to your security stack and is trashed by the rules.
Q3: Can I use this card's Opponent's Turn effect to reveal EX2-045 Calumon from my hand when my opponent plays a Lv.- EX2-045 Calumon?
No, you can't. EX2-045 Calumon is a card with no level, so it isn't considered to have the same level even though it's the same card, and you can't use this card's effect to reveal it.
Lv.3 Agumon Expert EX4-023 R Rookie | Vaccine | Dinosaur [Opponent's Turn] [Once Per Turn] When an opponent plays a Digimon, by revealing 1 card of the same level in your hand, place that card on top of your security stack face down. --- Inherited: -
Lv.3 Agumon Expert EX4-023 R Rookie | Vaccine | Dinosaur [Opponent's Turn] [Once Per Turn] When an opponent plays a Digimon, by revealing 1 card of the same level in your hand, place that card on top of your security stack face down. --- Inherited: -
Lv.3 Agumon Expert EX4-023 R Rookie | Vaccine | Dinosaur [Opponent's Turn] [Once Per Turn] When an opponent plays a Digimon, reveal 1 card of the same level in your hand, then place that card on top of your security stack face down.
Lv.3 アグモン博士 EX4-023 R 成長期 | ワクチン種 | 恐竜型 【相手のターン】[ターンに1回]相手のデジモンが登場したとき、自分の手札から、そのデジモンと同じLv.のカード1枚をオープンすることで、そのカードをセキュリティの上に裏向きで置く。 --- Inherited: undefined