First of all, we're not machines at all. Be organic and depend on organic matter for survival. We have trillions of cells, themselves all making decisions for their little part of the body. We experience emotion, we have compassion (some of us), we can reason (some of us), and we have the ability to understand ourselves well enough to go in an fix things if something goes wrong.

As to it being 'perfect,' well we've got the fun zone right in the middle of the sewage system... It's practical, but creates a lot of problems.

But in all reality, I don't think it's fair to 'dumb us down' to just organisms either. The body is fascinating. The things it can do... The human mind figured out music, and wrote the Ode to Joy. Ten fingers can traverse a piano keyboard, or a computer keyboard. It can produce art, build buildings, cradle the young. We can prolong life, make life better for others, and even when things go wrong with our bodies we still find ways to express ourselves in the world.

The body is an amazing mechanism with which life (our life) can express itself, and while it's not perfect, I would still call it a masterpiece.

It's no use discussing it with a theist. The best killer to their claim is the positioning of testicles. The only advantage to them being external is for cooling purposes or ease of removal , I guess. A well designed organism would have them in a far less vulnerable situation.
Joking, maybe not.
Theists choose to ignore science for their belief. There is no way to expect logic from them.

For such perfection, why so much sickness and breakdowns (physical and mental). And why does our shit stink so badly.

From an engineering standpoint, the knee joint is of a very poor design. That was just one I hadn't seen listed below. There are many others.

Ok, so why is the air passage and the stomach passage too close in the throat so we have the possibility of choking? Also what was that appendix really for except to cause trouble.? And the biggie, why do we age and wear out if it's perfect?