Hi Steve. A PO of my '71 had removed the side markers, and since owning it I've done all the mods you mentioned, plus removing all the emission equipment, fitted a Getrag 5 speed, power windows and recently the hard door pockets. Now, this may all be sacrilege to some, but I did it to suit myself, making it what I wanted. As I never considered the car an "investment", the resale value is of no consequence to me. In your situation, in view of the mods already done, you may as well continue, however, in the final analysis, the decision must be yours alone to make.
On a final note, Mine is definitely much nicer to drive, than when "original". Just my 2 cents worth. Dale.