You can see somewhere (in the Finances tab, i believe) what percentage of your transfer sales will be made available to you. I think at United it starts at around 60%, but can easily get up to 100% if you play your cards right.
It is important to look at the financial and off-the-pitch side of things if you want true success imo - so in your case, that extra £40m or so that "disappeared" was likely put into the bank account and hence used to pay off the club debt in part, or something like that.
As United, I tried to ensure that Old Trafford got expanded - twice in the first two seasons I managed to persuade the board to go ahead with the idea (which meant pretty low budgets in the meantime for wages and transfers), but when you are selling out a 100k capacity ground twice a week (compared to 60k) it is a pretty major boost to your revenue and helps in the long term.
Additionally, if you can make enough money, your debt will start to clear up a bit too. In my game at around 2012, good old Mr Gill announced to me that thanks to the improvements in the clubs financial state since I took charge, they had been able to pay off a sizable chunk of the loan. Not having those interest payments adds another big haul to my annual budgets.
Finally, in about 2013, Gill had to retire, and one of the Glazers (Bill?) won the election to step up and become chairman. In doing so, he injected another £70m from his personal wealth into the club.
D'Laryea would mark Bojan out of the game with ease. I think that's a given.
