I think a bike fit takes a lot of the guesswork out of your hands, it also gives a placebo esque feeling of satisfaction that everything is ok.
Thing is, bike setup is SO important. If you get it wrong, you get knee ache, back ache or any number of aches, and it could be a matter of cm's that makes the difference.
I personally think the two important things saddle height and bar reach are important, minor changes do make differences, for example the new bars are 2cm's wider and are more comfortable, but this could be the shape of the drops, I am more confident on the drops than on the old bars. I didn't really notice any difference between 172.5mm cranks and 170mm, nor any difference between clips and clipless.
I came across a tip for saddle bar length, and it quoted that "If you look down through the bars it should be in line with the front axle", my old bars the axle was always slightly in front, the new bars & stem it's in line so maybe that is what made things better.
I suffered a compression injury to my right leg years ago, and this has given me some problems, how ever as I have got fitter, this as become less of a problem, I presume as the muscle has improved it has given more support to the damaged area/s, clips or clipless has made no difference.
Cleats, when I put them on, I just put them on so they are in the same place on the shoe, and felt right when attached to the peddles.
The rest backache, numbness ect.. I think improves with fitness.
I got off the bike last night and it didn't feel like I had just done 40 miles, apart from some ache in the thighs, due I think to the maintained increase in cadence.