When you make a closeup picture at f16 you're not going to have much depth of field. So a lot of the image will be soft looking unless it is a very flat plane. Do the focus testing first and if it comes out OK try to take a similar picture using f-stops from 16 to 64. Compare those negatives to see if depth of field has something to do with your problem.
Another approach is to measure the distance from something on the front standard to the surface of an installed film holder with a sheet of film in in (or something the same thickness as film). Then measure the same to the ground-side of the ground glass. You can use apiece of thin cardboard and draw a line for the first measurement, then use the same piece for the second measurement. If the ground glass is backwards, it will show up as being off by the thickness of the glass or perhaps the fresnel too if that's in the wrong order.
I use a lens board without a lens in it for the reference, but any definite edge or surface on the fronts standard will do. Make sure the measuring stick is perpendicular to the film plan in both directions (side-to-side, up and down). When it is, you will have the minimum distance for a given measure.
Good luck!
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