Hi Ralphile, build looks excellent. It will take a little while to fine tune the axe and for the neck to set in.
So presume this is the stock plastic nut ? To lower the slots you can use the top 3 strings E A D like dental floss and file them down a little. If you think all the strings are too high at the nut end then best you remove the nut and run it over 80 grit paper on a flat surface to lower the profile of it. If you remove the nut you might as well upgrade to a bone nut will sound heaps better.
There are about 3 or 4 different profile and width frets and I'd say your strat copy frets are worn down. There is small, medium, large and jumbo and different widths available. Your tele build frets probably seem high as they haven't been used and worn much.
Did you manage to get some stain on the fingerboard between 15th and 16th fret ? You should be able to sand or steel wool this off, wrap some 1200 paper around a rubber eraser works well.
Looks like you evened up the stain depths alot closer on each sides of the 2 piece body.
Have you intonated the bridge yet ? could be the reason your low fretted notes aren't in tune. Hopefully the bridge saddle screws are long enough as you haven't modified the bridge pup cavity so the bridge plate moves closer to the pickguard