3 Questions
 

1. What happened 3000 years beforehand, and are the events tied to what happened in Wild Force?

2. How was Kendrix restored in the end?

3. How are the villians possible,since the Z-waved wiped the universe of all evil?

Re: 3 Questions
 

1 Possibly they could be related, but it was never specifically stated. By the time Wild Force was being filmed, the majority of the show was under Disney's control and they didn't want a lot of ties to previous seasons... so, who knows.

2 Dunno. Perhaps her essence was transported to sort of a limbo via the quasar saber and when everything was restored, it released her. Honestly, though, you just kind of have to accept it... like Andros' tears restoring Karone to normal in Space.

3 The villains from the series originated outside of our universe. Thus, part of the reason this is "far, far away, deep in space, to a galaxy unknown." It was outside the reach of his powers. Similarly, Lightspeed's villains were sealed away and from the past/different dimension, Time Force's were from far into the future, etc... to explain why they were around. Some other shows since then... well... I dunno.

Re: 3 Questions
 

1. No one knows what happened 3,000 years beforehand but it wouldn't have anything to do with the Ancient Warrior situation in Wild Force since that was 10,000 years beforehand.

2. No one is quite sure but the Quasar Sabers appear to be powerful artifacts if they're capable of restoring life back to Mirinoi so perhaps her Saber had something to do with it.

3. It's a case of not all of the villains being destroyed for various reasons since Zordon never said he was going to rid the universe of all of the evil since that's just not possible.

2. That's a good possibility since her 'spirit' was seen going into her Saber before it was sent flying away.

3. I agree with you there. As I said Zordon's energy wave likely was only responsible for destroying the ones that were currently active.
Not to mention some future villains were unaffected by it for various reasons.

Scorpius, Trakeena and Mutiny = they were in another galaxy that was considered to be lost.

Diabolico and his demons = they were sealed so they weren't a concern.
Ransik = He came from the future so he wasn't alive yet.
Orgs = Only Toxica and Jindrax were around an they wouldn't have been a threat without their Master.
Lothor = He was likely still in hiding so he wasn't a threat.
Mesoogog = hadn't been created yet.
Gruumm = wasn't a threat yet.
Underworld = they were sealed.
Moltor and Flurious = they were sealed.
Dai-Shi = he was sealed.
Venjix = he was in an alternate dimension.
Xandred = He and the other Nighlok were sealed.

Re: 3 Questions
 

I don't remember about the Fearcats. Kamdor was sealed but I don't think it was ever said about Miratrix but whatever the case it didn't matter since they weren't seen as threats until they became active due to the Corona Aurora's presence.

The Armada weren't seen as threats same thing with the Warstar since they were faraway.

Sledge was too faraway.

Not sure about Arcanon but I'm guessing he was too faraway or just didn't care.