Norland Excell Source/Detector Alignment procedure

Hello to everyone in the forum. After replacing a broken shutter switch on the filter assembly of this Norland Excell densitometer we're getting many "Retrying" messages while performing the initial/daily calibration, and when it ends it shows Precision: OK, Accuracy: OUT OF RANGE. We got the 388S631 service document and for the alignment it mentions to use an "Align" program from the XSST menu. There isn't such menu in the DXA Utilities program so the question is which function should we use there in order to center the beam (Count rates maybe?), and how to proceed with the detector and source alignment without getting too much radiation in the process?
A comment: one of the filters lenses is white, while the other two seem to have a grainy white powder on them. We tried to clean them up with a cotton swab but the "powder" seems to be "inside" somehow and not in the top/bottom surface of the lenses. Does that mean those filters need to be changed? Could it be related to the accuracy problem? Any tips will be more than welcome, thank you.