Temporary Solution:
When you've paid off your debt, save and quit.
Next copy your save files to Doubutsu No Mori (J) [!].fla and .mpk respectively.
Then, load the japanese version, talk to tom nook to upgrade your house, and either wait until the next day or just change the clock.
Load the japanese version again and be sure your house is upgraded. save and quit, copy the japanese save back to the english version name, and enjoy your upgraded house.
Btw ive noticed that for the debt after the first upgrade that it cuts off the 100k and just makes it the 49782 or whatever.
Also, when i do the upgrade in the english version, it wont load in the english version afterwards while it loads in the japanese version without the house upgraded.