First, regarding the Darwinian theory of evolution of species: it is pointless to go through the numerous flaws in this theory point by point here; they have been enumerated ad nauseum elsewhere. Suffice it to say that alternative theories have far more merit.
Flawed it no doubt is, as any theory inevitably is; I doubt though that the flaws are as numerous as you suggest, and am pretty sure that any alternative theory has many more. If there is a theory that is at the same time simpler and more powerful than Darwinian evolution, I haven't seen it yet.
As you have rightly stated, alternative explanations raise even more questions. That is correct; but so what? Do you reject alternatives because they raise questions? On that basis, Darwinism should have been consigned to the dustbin a century ago. Unfortunately, it still persists as an embarrassment to science.
Yes, theories are rejected when they raise more questions than they answer. It is called Occam's Razor: theories should be as parsimonious as possible. Throughout history it has been proven that the simplest theories (i.e., the ones making the fewest assumptions) tend to be the correct ones. E.g., the Ptolemean model of the cosmos, with Earth at its center, worked fine and predicted the positions of planets admirably; but at the cost of complex mathematical descriptions to explain the weird, spiralling motions of the planets along the sky. Copernicus found that the mats became a lot simpler when you assumed the sun, not the Earth was the center of the universe, without any loss in predictive accuracy. Unlike the Ptolemean model, this enabled him to actually explain the reason for the apparent erratic motion of the planets. Keppler, finally, demonstrated that theory and observation reached a perfect match if you assumed that planets revolved around the sun in slightly elliptical rather than perfectly circular trajectories. And he was right.
Evolution, too, is a very simple theory, consisting, essentially, of just a single principle. Yet its explanatory power is huge. So is the evidence base supporting it. Sure, you could do the same explaining by assuming it was all designed by some sentient being, but that really doesn't answer anything at all, does it - it only shifts the problem, and adds to it by assuming without any evidence, (and worse, without any necessity) the existence of such a being. Try this link
for a more considered exposé.
The larger issue is that it must first be agreed that a phenomenon exists, and that that phenomenon needs investigation. Having come to that agreement, then the next step is to devise a method to study that phenomenon. Intrinsic to that method is the equipment.
Agreeing the phenomenon exists seems to me a strange way of starting research. Hypothesizing
that it may
exists is the scientific way to go - you are doing your research to find out whether it exists or not, don't you? In your hypothesis, you should make clear what the unique characteristics of the phenomenon are (and also, where you got that information). Then you need to wonder how these characteristics could be measured in a way that is valid, repeatable, and unbiassed. Finally, you need to think what equipment you may need to do this.
As you say, research into ghosts still remains at the absolute beginning. There is no scientifically sound evidence at all that lends any statistical weight to the likelihood that the supernatural exists. You claim it is very complicated to do the research, but that I find hard to believe. Just look at the experiences told by people on these boards and elsewhere. They involve highly concrete, perfectly measurable phenomena. The only thing that needs to be done, as you rightly say, is to separate these observations from the observer. I suggested one setup in my previous post for doing this; many more can be devised.
Extraordinary claims demand extraordinary evidence. (Carl Sagan)