First, to answer the question "How many problems are caused by mods?" None, zip, nada. As with most things, do it right and it will work right.
"Why reinvent the wheel when Ford and his engineers did a hell of a good job the first time around?" Because I can, and I will also note, so did Ford and his engineers.
"But, seat belts, a fuse and battery cut off switch will stay." Hence, you drive a modified A.
"the drums and maybe a MILD higher compression head like what Ford offered in 1931.
KISS---Keep it Stock Stupid!!!"
The last time I landed on the fence like you just did I nearly passed out and I thought my child making days were over.
My car has a number of "improvements", many by others some by me. I don't understand the need for a 12 volt system but it was there already. I'm not sure about the use of the alternator either, especially since the car came with a freshly rebuilt A generator. I do know that in the process of changing these items they sure didn't understand automotive electrical systems. The majority of the mods that I did were performance oriented and a repeat of what I did 55 years ago. This time they worked. I am a firm believer in "To each his own" and when it comes to the purest among us I have nothing but respect and awe at what they have accomplished. I could possibly do likewise but it is not in my nature. So I will stick with my car and enjoy it to the fullest without ridicule to those slower than I, albeit "more original". I can appreciate the artistry without having the brush shoved down my throat or being thought less of to support shaky egos. Like Frank sang, "I had it my way".