You can edit the image properties (Image ▶ Properties...) to set the Z, T and C lengths. But in some cases this will not work depending on the order the image planes were imported.
There are many different sorts of metadata. The most important is the structural kind—dimensionality of your images and so forth. Without that, you cannot process them properly. The physical calibrations are also important if you care about real-world measurements. Other than that, things like which detector was used, what magnification, etc., are all nice to have, but not necessarily crippling to be missing, depending on what kinds of analysis you are performing. (As an example: if the PSF were present in your metadata, this is an extremely useful piece of information for algorithms like deconvolution, but not needed for many common things like thresholding.)
In general, no. Bio-Formats does have a "metadata only" mode which you could use to read and display the metadata, but you'd have to write code to attach it (somehow) to an already-imported image.
It would be much better if the performance of Bio-Formats could be improved. You could send a bug report to the Bio-Formats team requesting someone investigate speeding up the Prairie file format import. IIRC, the Prairie format's XML file enumerates the TIFF files containing the image data, and so doing a file listing in the directory seems superfluous to me. If that step could be cut out of the process, I am guessing the performance would improve dramatically in your case.
Even better than that would be if you could record in a format other than one-TIFF-per-image-plane, which is known to have these problems when the number of planes gets large.
That is unfortunate; the performance of SSDs is dramatically better.
Ah, then I am not sure what else you can do regarding that. It might be related to how Windows handles file locking, which in my experience is slower than how macOS and Linux do it.