Hi Kaitatzi Myrsini
1. Yes and no. If you have major differences between the local structure and the average, then yes, we would expect lower Rw when refining the local structure only. However few things to keep in mind! You are refining the structural parameters in both cases, so in principle, the fit could modify the structure obtained from the Rietveld refinement to fit the local structure well. In that case the Rw could be lower for the 10 Å fit. If you have little or no differences between the average and local structure, then it is completely normal to get higher Rw when you fit fewer points. In general, PDF fits are always worse than Rietveld fits because the Fourier transform put the noise on all points in the PDF.
For your other questions, the most important thing to remember about L.P. is that any L.P. obtained from both PDF and Rietveld refinement are never correct! The only case where you can get absolute values for L.P. is if you have an internal standard (such as LaB6 or Si) mixed into the sample. The L.P. values are correlated with a bunch of experimental factors, such as sample-to-detector distance. In Rietveld, we refine a separate parameter, zero error, for example, but in PDFgui we do not have such parameters. So basically, always refine L.P. in PDFgui. The deviations are because of these experimental factors. So doing this kind of direct comparison between PDF and Rietveld is almost meaningless. It is good to do it, but deviations are difficult to use for a whole lot. (This also goes for comparison between different Rietveld refinements of diffraction patterns. Unless you have an internal standard, then deviations could easily just be differences from the measurements themselves)
The limits for deviations are not easy to say. Mostly because in the PDF the atomic positions and L.P. will correlate, as opposed to Q-space where they are not correlated. The most important thing to do is to ensure that the fitted model is physically reasonable.
The same goes for U factors, unless you have neutron diffraction data to high Q, then do not trust the values of U factors in both PDF and Rietveld refinements. They correlate with a bunch of different things and are usually fixing a bunch of stuff not described anywhere in your model. Neutron scattering is usually the only data that allows for the refinement of anisotropic u factors.
U factors are temperature sensitive. I do not know what temperature you are measuring at. A u factor of 0.08 at room temperature is very high for a Fe atom. I would, first of all, see how much worse the fit becomes when you just use Uiso. If it becomes much worse, it must be because the model wants to broaden those PDF peaks. I would then check if it could be from stacking faults, a split atom site or something similar that causes the electron density to be smeared out.
Regarding the minority phase, I think there is only one way to find out. If you fix the Uiso to something reasonable, does the fit gets much worse? If yes, then we need to look at why it does that.
Also remember that you have a instrumental contribution to the PDF peak width, so make sure to get a standard and refine Qdamo and Qbroad.