Some issues,
Need to fully solve the fuel related issues, can you find a second hand fuel tank with traditional vented upper fuel cap ? When the combo runs with trim set at neutral independently if sits slight less or more than 90 deg with deck load well distributed, does the prop aerates ? what about at tight close turns at speed, at Non Flat water conditions, does the prop aerates more ?
So the boat had a long shaft transom for a long shaft motor use and was lowered to use a short shaft motor. Who did the transom mod, the previous owner or yourself ? For clarification, can you post a pic shot from inside the boat showing how the motor sits and bolts on transson while at 90 deg ?
Been using CRC liquid gold decarbonizer in a can for years now.. That's what your motor needs to run much smoother as assume that never before has been decarbonized by previous owner. No need to install new saprk plugs, current ones have very few run hours from out of the box, can clean brushing them off with a hard toothbrush soaked in paint thinner for at least 2-3 times in a row.
Happy Boating