Vinegar shouldn't hurt a thing as everything it would come in contact with is plastic (Pex Pipe) rubber, etc. Exception will be the water heater but it most likely has the most scale buildup so the vinegar will attack it instead of the tank itself.
Pretend you are winterizing and just use the winterizing port to suck in some vinegar straight from the jug. Open faucets one at a time until you smell vinegar in the water coming out. Let it sit overnight then flush well with water.
For the faucets, remove the aerators and shower head. Soak these for a while either in Vinegar or CLR, following the CLR instructions of you use it.
Not much scale will stick to PEX or in the water pump. Faucet outlets will make it noticeable and the most buildup will occur in the hot water tank.
BTW, remove the filter element first and when all flushed out at the end, replace with new.
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2018 Flagstaff Micro Lite 25BDS
2004 Nissan Titan