Prepare Form doesn't recognize check boxes

One other consideration before recreating all of those fields is whether they should actually all be checkboxes.

I've developed interactive Acrobat PDF forms for many years and recently ran into a situation where I initially used checkboxes for several related choices, but ultimately replaced them with radio buttons because only one choice was supposed to be selected.

As a general rule, checkboxes are appropriate when more than one choice can be valid at the same time. If only one choice from a group should be permitted, a radio-button group is usually the better field type.

With dozens of boxes on each of your forms, it may be worth reviewing the original forms before recreating everything. If some groups represent mutually exclusive choices, this could also be an opportunity to improve the form design rather than simply reproducing the original paper-form layout.

The field detection doesn’t always work and sometimes confuses radio and check boxes. 

I usually try it and determine if it’s easier to fix up or do it from scratch. 

(I would never do a form in Word. InDesign can create PDFs form fields but you will still have to finalize them in Acrobat.)

The Forms Wizard is what it is - sometimes it works great, other times not at all. I would not go through the trouble of converting to Word and then back to PDF - you already have PDF files that somewhat work. Converting a PDF to a form is _NEVER_ simple, and always requires additional work. There are tools built into Acrobat that make this easier - you can for example several copies of the same element at certain intervals, you can copy and paste a group of form fields, you can place the same field on every page in your document and so on. Use these functions and after a few forms, it will not look that complex and labor intensive anymore.