ok:
1) lower the size of joints of the skeleton (file -> preferences -> jointsize to bout 1 or 2)
2) assign everything correct, how?: select the part of the skeleton ( bones) and look at it where it is, than select all vertexes that match the bone system of the selected bone, than click assign, do this with all bones till tehre is nothing left to assign
3) to put in all anims i suggest this: copy the model you want the anims from (same model as the one you got the reference-skeleton of) in a new folder on ur desktop decompile next things = qc-file, reference and sequences, now it decompiled all animations in the same folder, now you have to export the modl you have now to smd and save as reference in the same folder as the decompiled models (with qc file, ref and seq files) (save as referenve under same name as original reference-smd)
4) copy all the textures (!!! 8 BIT !!!) into the same folder as the anims and ref and qc file
5 go to milkshape -> tools -> half-life -> compile QC file and select the qc file in that folder
now it should run all the animls and textures etc and when you look in the folder there is a nice .mdl file