@MelonHead he can still have his sword, thats no problem, and maybe you can make his flintlocks into badass modern day custom musket style pistols or whatever. and Zai matsu isnt ridiculosly strong with the suit, Id say 2.5 strength and speed of his normal human body, he is technically super human but still very mortal.
You can see Isaac's modern day equipment in his CS, if you still want to fight him with this load-out you can.