There's a few approaches that occur to me. I've redone the March Harrier for my T5 campaign (see my blog if interested), and it came in at MCr101.9.
Firstly, the remaining 75 tons (or 18.75% of the ship) could be owned by other traders, perhaps also crewing the ship; thus, the only consideration is profit-sharing rather than paying off the finance.
The second approach is to say that the rest is owed to the bank. But if 18.75% of the value of the ship is owed to the bank, there is a simpler process than amortising a loan. Remember the ship needed a deposit of 20% - MCr20.38 in our example. Thus, of the 81.25% owned, 20% of the ship is represented by the deposit, and so 61.25% of the 480 monthly repayments have been made, i.e. 294 payments have been made; there are 186 to go at Cr424,583 each.
On subsidies, I am still experimenting but it seems that the Classic Traveller rule is a reasonable guide: no repayments by the team working the ship, but half of all profits are remitted to the subsidy holders.
I am still working out the operation of the ships accounts because it is not clear to me what the on-going life support costs are (in Classic Traveller it was Cr1000 per person per 2 weeks, Cr100 if in Low Berth). If someone could point me towards a page number, would be most grateful.