A few changes....
Sigma 13/Yanagi (Cardamine) -> N. Berlin
N. Berlin(Light Arms) -> Yanagi
Profit = 2678095
It takes less than a minute each way.
Only problem is you have to be careful of the Junkers on Yanagi. If you take off from Yanagi and they demand you drop your cargo then you'll have to get a bribe at N. Berlin to make your rep better with them.
Other one...
N. Berlin(Diamonds) -> N. Tokyo
N. Tokyo(Prisoners) -> Yanagi
Yanagi(Cardamine) -> N. Berlin
Profit = 9199404
This takes a bit longer. Probably as long as the route your doing now but there's no issues on the route with pirates.
I'm just a shade under 100M right now. Coulda easily reached it by now but I can only play for a short period at a time.