Hi Amid, what Scott said.
The second batch of photos you posted you have improved the fit, just needs a bit more sanding so all the faces are flush, including bottom of the neck pocket.
Maybe you need to sand it with a lower grit paper and remove a bit more excess under the fingerboard. Work out which places are causing the gaps and sand those areas.
Do a trial fit fairly regularly so you don't oversand.
Once the heel fits flush you can do a mock build as Scott suggests to check what the string action will be.
These kits have about a 4 degree neck angle to compensate for the high TOM bridges