Totally forgot about having asked this question, but fortunately I've been able to solve it. The were two problems: my integrator wasn't up for the task and you do have to include the Sun in a free return trajectory simulation as its gravitational influence on the Earth Moon system is not negligble, even on the time scale of days (at least with the integrator that I employed).
Here's the data I used for the scenario (Apollo 11, fetched from JPL Horizons), where g is the gravitational constant and dt is the time step. AUs for distance, years for time and solar masses for masses:
export default {
name: 'Apollo 11 - Free Return Trajectory',
g: 39.5,
dt: 40e-7,
distMax: 0.00713911058,
distMin: -0.00713911058,
distStep: 2.3797035266666667e-6,
velMax: 0.5,
velMin: -0.5,
velStep: 5e-6,
rotatingReferenceFrame: 'Earth',
cameraPosition: 'Free',
cameraFocus: 'Origo',
freeOrigoZ: 16000,
massBeingModified: 'Sun',
primary: 'Earth',
maximumDistance: { name: 'Moon to Earth * 10', value: 0.0256955529 },
distanceStep: { name: 'Moon to Earth / 100', value: 0.0005139110579999999 },
scenarioWikiUrl: 'https://en.wikipedia.org/wiki/Free-return_trajectory',
masses: [
{
name: 'Earth',
x: 0.4240363252016235,
y: -0.9248449798862485,
z: -1.232690294681233e-4,
vx: 5.622675894714279,
vy: 2.5745894556521574,
vz: 3.8057228235271535e-4,
trailVertices: 2e4
},
{
name: 'Sun',
x: 0.004494747940528018,
y: 9.145777867796766e-4,
z: -6.127893755128986e-5,
vx: -1.7443876658803292e-4,
vy: 0.002043973630637931,
vz: -4.697196039923407e-6,
trailVertices: 2e4
},
{
name: 'Moon',
x: 0.4220528422463315,
y: -0.9230209264977778,
z: 1.632323615688905e-5,
vx: 5.486589374929882,
vy: 2.420601498441581,
vz: -0.014677846271227611,
trailVertices: 2e4
},
{
name: 'Apollo 11',
x: 0.4240447232851519,
y: -0.9247715402118077,
z: -1.129301018611092e-4,
vx: 4.395253850175561,
vy: 3.8323649107803948,
vz: 0.15792573886687206,
trailVertices: 15e4
}
]
};
export default [
{
m: 0.000003003,
radius: 91.74311926605505,
color: 'limegreen',
name: 'Earth'
},
{
m: 3.69396868e-8,
radius: 22.93577981651376,
color: 'grey',
name: 'Moon'
},
{
m: 0,
radius: 1.2,
color: 'limegreen',
name: 'Apollo 11'
},
{
m: 1,
radius: 90000,
type: 'star',
color: 'yellow',
name: 'Sun'
}
];
And the result