You're right on the money in terms of commuting upgrades. Buying used bikes is a great way to go about acquiring a ride, but sometimes bikes need a bit of refitting for commuting.
I took a look at the 1981 Miyata Catalog. Models from year to year are generally similar, so this should be accurate for most late 70s early 80s 912s. This bike is described as a "fast sport rider for racing-oriented cyclists," meaning that it isn't going to fit fat tires, fenders, or racks too easily. What is important is the distance between the tire and the frame.
You may be able to get away with a 700c x32 tire and narrow, metal fenders. Metal fenders are a bit more expensive than plastic, but can be bent to fit into tight places. Note that most fender manufacturers specify 10mm clearance between the tire and the fender, so as to prevent a pebble or twig from tearing your fenders off. There may or may not be braze-ons for fenders or racks, but that is easy to get around. Lots of bike shops sell metal clamps that secure everything to the stays quite well.
If you're comfortable with the largest possible tire being ~32mm, go for it! Understand, however, that bikes designed for skinny tires and no fenders may be difficult to fit. If you decide not to, look for Touring or Sports-Touring models which always have clearance and braze-ons (In this catalog, the 1000 and 610 are both touring models).
One alternative option that will require more work is to convert the wheel size from 700c to 650b. This will involve new wheels and long-reach brakes, but it will allow you to run fatter tires and fenders with no issues.