Wojtek is right about the pics Harrison - try to light them from the angle where you're taking the pic. Don't rely on flash alone, as this can 'wash out' detail etc.
Concerning the filler; the first pics you posted showed the gap at the fuselage joint as much less than in the later pics, so Wojtek is right again - CA would have been better. But, I think Wojtek is again right, in that the fitting of the fuselage halves could have been better - possibly caused by mis-alignment of some of the internal parts. Always test fit and check alignment.
The 'mix' of the 'porridge' filler looks about right, but the idea is to run this into the gap, wiping off any excess, then repeating as required. It'll make it much easier to sand afterwards, and the first application will form a 'bridge' in the gap. The 'porridge' is great for very small joints or gaps, where putty or other fillers would be difficult or impossible to apply without lots of excess all over the place, as it's intended to run into the gap, build up, and then harden. But for larger gaps, a 'stiffer' filler is required, from CA glue to something like 'Milliput'.
As for the fitting of parts, it's essential to check every area of a kit before commencing work, in order to know 'what's what', and where, and how, other parts should fit. Always spend time test fitting before even thinking about construction, as this will, or should, indicate any potential problem areas or defects, which can be corrected, or allowed for, before the assembly. The time spent doing this is never wasted, and actually saves a lot of time, frustration and possibly a ruined model in the long run.
Test fit, test fit and more test fit!!