"I will be installing my microwave into the wall"

Please be more specific about what you mean by "into the wall". There is no way for anybody to know what you intended by that description.

The Whirlpool installation instructions for its WMT55511K and WMT50011K built-in microwave ovens require that the ovens should be installed at least 36" above the floor.

How are you installing a "freestanding" oven in a wall? Countertop ovens require ventilation on the sides, top and back as described in the user guides.

Pantry is on the other side of the wall. A frame will be built. Just wanted to know what would be a good height. I prefer something higher than 36" (normal height if it is just sitting on a countertop) and 54" is too high. Side-swing door.

You need more than a "frame". You need full cabinet, with floor, and surround, to attach and support. Plus the correct trim kit, that provides ventilation.

When I had my kitchen renovated a few years ago; both I and my kitchen designer, put a lot of thought into planning for a microwave shelf. I use my microwave often. I wanted a shelf that could accommodate different sized microwaves, in case I needed to replace it in the future. My shelf is 54” from the floor. It is a good height for myself (I am 5’6”) and for my husband (he is 6’2”). I have a galley styled kitchen; one side has my fridge, range and dishwasher. The other side is all upper cabinets, and below the counter are 3 bays of 3 sets of drawers. The microwave shelf is in the middle of the upper cabinets. I also have a dedicated outlet behind my microwave shelf. We are quite happy with our microwave shelf and its placement. Best of luck on your journey!

A freestanding microwave height would be the height of your counter- or whatever other cabinet/table/shelf/ect surface you want to place the microwave on. You could put it on a shelf/other at 42" if you want, make sure the shelf is big enough and supportive enough to handle it. And meet venting clearance. I assume this would not be over a 36" counter- that would be kind of silly to build in a shelf in the wall six inches taller than the counter.

If you just want it six inches higher, maybe consider having a six inch tall box built instead to sit on your counter with the freestanding microwave sitting on it. Have it with a drawer in it to store stuff.

You might consider the slim, Whirlpool WMT50011KS 30 Inch Built-In Microwave Oven which requires a simple box to contain it and includes a slim frame to hide the gaps between the oven and the surrounding box (see page 5). If it were installed over a range like its OTR sibling, the bottom of the oven would be about 50" from the floor to protect it from heat from the range. But you won't have a heat source below the oven so you could install it lower.