If it's a long term hold then sub metering is going to best the best way. The upfront cost can be significant (as you've found) but also does technically increase the value of the building (using the income valuation approach).
Depending on the age of the building be careful about any work being done on the panel. Some City's will come in and require that you bring the entire building up to code. Higher chance of that with a multi-unit property versus a single family. Depending on what year of the NEC the City follows it could mean full AFCI/GFCI and tamper resistant outlets. A massive cost that basically requires either a full rewire of the building or potentially extensive troubleshooting.
There are a number of companies that will go read meters and bill the tenants for you. So while the account needs to be in your name these companies will basically do the billback for you. And with sub meters you can bill back 100% of the cost (whereas for water and electricity most places only allow a certain percentage if its not sub metered).
I think if you calculated your numbers based on a cash on cash return it might surprise you, plus would give you more cash flow so ideally helping you to qualify for larger loans on subsequent investments.
If you used a 20% return method based on $200/mo then you would be looking at being able to spend $12k or 3k a unit. I don't know how pricing looks in your area, but $3k a unit would come very close to getting it done for the furnaces but not the water heaters.