Everyone who has answered is more experienced than I am at doing this. So far, finding the "idiot proof" finish has eluded this idiot...So please take this FWIW, and if there is any controversy take the other advice!
One thing you mentioned is that you get lint spots where you take the rag off. I have started to use a little shellac (an idea I got from McCreed). Most of what I have read says (a) don't stop until you get to an edge and (b) don't let the cloth get tacky. Maybe the same is true with other wipe-on finishes?
As mentioned by others wipe on finishes are generally VERY thin. Also if applied to bare (or dye stained) wood, a lot of the first coats gets soaked into the wood which might partially explain why you see a color change, but the finish may still be super thin. The change in color can make you think the finish is thicker than it really is since some of the color is below the surface of the wood.
I am wondering about something you said about the way you are applying coats. I think you said that you apply when the underlying coat is still a little tacky and you sand every few coats. With minwax, as well (as with the acrylic I use) the directions are to let it dry for 2-3 hours, then sand lightly with 220. by that time it should not be tacky. I have never applied a 2nd clear coat over a tacky finish, although I have heard of doing it with paint.
Others may correct this, but I don't sand flat between coats. I just lightly "scuff sand"... I just make the surface slightly rough enough so that the next coat of finish sticks to it. I try not to flat sand until I have a lot of finish built up. If you flat sand between coats you may be sanding away too much finish, and will most likely need more coats.
What JimC said about "spots" resonated with me. Especially on my ES bass. The place I sanded through was on a "bump." Inadvertently, I was putting more pressure on the top of the bump than on the valleys and sanded right through. For the finish I have been using the mfg liked sanding pads like the Scotchbrites you mentioned. I have found that it is really easy to put more pressure on a high place or a curve than a low place. So any place I have a high spot, I now try to sand without putting much pressure on the pad. lightest of all on a run or drip. It takes a LOT longer, but I haven't yet had an accident with my current build.
All thought to put in the FWIW column ;-)