from slide area values to points... I think! that you wanted to select the values in that file that had -9999 in them in some field... from there, you make that selection permanent by saving (copy features perhaps) to a new file... from that file, you wanted to do a field calculation to change the -9999 values to some other value that is too far up for me to scroll to tonight. That last step, the field calculation.
Now during this whole process, did you set your analysis properties in the tools... or as a parameter in your model... to a certain 'extent'.?? You need to. You cannot assume that the extents of the analysis have anything to do with what you see on screen. Set analysis extent to be the width and height of the data that you need to complete the analysis.
As far as modelbuilder goes... do it manually, get it to work, record the exact workflow including setting parameters for analysis properties and the like. When the manual steps work, that is exactly what you have to replicate. I see way too many people trying to get a model to work and it is the boring stuff that causes it to fail..( e.g. extents, coordinate systems, cell size, snap rasters, selection types... the list is long and not all these apply to your case)
Good luck