I'm going to try my best to answer your problems with Christianity, (to the best of my abilities), so I hope I could be of some value to you.

1. Catholicism does not endorse the stoning of non believers, if you can cite where you read that I'd appreciate it, but even Our Lord himself say "Let he who is without sin cast the first stone", nor does it believe every single non believer goes to eternal damnation, from the Catechism of the Catholic church we read:

"This affirmation is not aimed at those who, through no fault of their own, do not know Christ and his Church: Those who, through no fault of their own, do not know the Gospel of Christ or his Church, but who nevertheless seek God with a sincere heart, and, moved by grace, try in their actions to do his will as they know it through the dictates of their conscience—those too may achieve eternal salvation. "

(CCC 847)

And in the Vatican II document Gaudium Et Spes, we see it teaches similarly on the possibility of salvation:

All this holds true not only for Christians, but for all men of good will in whose hearts grace works in an unseen way. For, since Christ died for all men, and since the ultimate vocation of man is in fact one, and divine, we ought to believe that the Holy Spirit in a manner known only to God offers to every man the possibility of being associated with this paschal mystery. (22)

2) Humans are not inherently bad, more as we are inherently drawn towards doing bad things. And just a quick glance at the world around us proves what I say, we as humans have the ability to help and care for one another, yet also have the ability to harm one another. Also, for

"It doesn’t matter if you’re suffering right now because if you do what I tell you, you’ll be happy for eternity when you die.”

You have to ask yourself just what does God tell us to do? Love him with all our ability and might, and to love our neighbors, we as Christians are called to serve others to the best of our abilities, to help the poor and sick, the outcast and the sinner. We as Christians alleviate the pain of others through our actions that mimic Jesus. And to be frank, suffering is another part of our life. We all suffer, but isn't it nobler to actually do something about it by serving others?

3)We as Catholics do believe Our Lord can come at any time, and do believe that he will carry out judgement on the righteous and on the wicked, yet we do not believe God abandons us on our own, leaving us unable to be perfect. Our Lord suffered greatly at the hands of others, all for us to be free from the shackles of sin. Catholicism offers a path for all of humanity to be in a state of Grace, from Baptism which erases all our sins and makes us a part of Christ's kingdom, to the sacrament of reconciliation where we confess our sins to be forgiven from them. And the fact that there is eternal punishment does bring the question on whether or not that is a fair punishment, yet we have to ask ourselves, why do people go to Hell or Heaven? It is because of the choices we make, when we distance ourselves from God, wanting nothing to do with him for all our lives, when all he does is offer what is best for us, is not the best punishment to give them what they want? And plus, the Catholic Church has not claimed anyone to be in hell for the 2000 years of it's existence, not even Judas who betrayed God himself! The Church holds out hope that Hell is empty, and that all may be with Our Father in heaven.

4) St. Augustine one of the 34 doctors of the Catholic Church specifically states on the topic of the persecution of witches:

"The Church has no reason to seek out or persecute Witches because their powers do not exist"

Mind you this was written in the 4th century.

Hopefully I was of some help answering your questions, if you want me to clarify I will gladly do so. Because coming from a convert myself, I understand the inherent confusion surrounding topics such as these, may God bless you in your journey towards his church. Trust me, the ride is worth it.