I don't think there's a problem.
On income, you do take the difference in the two corruption numbers, as the first number is extra income from "administration" (governors benefiting their settlements), not waste from corruption.
On the upkeep, I think you have assumed the Emperor and Prince have bodyguards cost 250 florins each, when in fact they cost 388 and 338. The difference is the 226 you are short of.
But I sympathesise - if it is this messy with only 6 settlements and no orders, imagine what it will be like after 6 months.
Calculating how long it took us to play WoS today, I did wonder whether we should be streamlining the WoS model rather than making it yet more complex. However, I would persevere with this because the whole point of a trial is to see if it is workable. And I really don't see any easy half-way house between decentralisation at this level and giving all the money to the reigning player to allocate.
BTW: do you want your character to take Nuremburg as his Duchy? If not, I suggest we treat it as belonging to a Count with an Imperial patron, rather than an Imperial city per se.
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