The diagram for loading can be misleading - it is relative to the reference_datum_position, which must be taken into consideration. All the various loading, contact points and other measurements are relative to it, and does NOT have to represent a real life cg position.
I usually modify my fore/aft loads to a point slightly forward of the reference datum, make them all the same and see how it goes. Try starting out at the empty weight cg longitudinal position. That way you just increment that one longitudinal value (same for all load positions) for further improvement. I look for good flying qualities, not particularly interested in loading up 250 seats etc. in a real life scenario. I typically just combine everything in about 3 to 5 positions:
crew (pilots/ cabin)
1st class pax total
coach pax total
baggage split fore /aft if applicable
cargo as desired
I use 170 lbs per pax, 40 lbs baggage each; 250 lbs total per pilot, 200 lbs total per flight attendant. Others use 175 /55 etc.
As an example, a 5 person crew of 2 pilots / 3 cabin crew would be 500 +600 = 1100 lbs for my
station.0 = 1100, x, y, z , crew (2+3).
Anyway, whatever. You can use the same technique with fuel tanks if you care to.
It is very easy to vary your loading when starting out - your setup will be default, but changing your loading values is quick and easy in the fuel/payload screen using your assumed weight values for pax, baggage, crew.
Regarding flap pitch - too often the designer just uses the default value of 1, which is lazy or an oversight because some pitching moments are absurd. I flew for the Navy for over 20 years, including test pilot school and have an FAA ATP - never saw anything like some of the flap pitch up changes I.ve seen in some FltSim models. In fact, some military and civil aircraft have a minor nose down pitch tendency. Admittedly, there are some designs that have had a flap / elevator interconnect scheme to counter a nose up pitch.