The car has power the lights/radio work but the car wont crank. What all hooks to the stock starter is there only one wire and its the positive cable from the opposite post of the battery on the relay? Does the starter have its own ground im missing?
the starter ground via the motor.
info is for the non mini starters (around 92 or whenever they changed), but should be close, if not the same:
find the solenoid. put car in neutral. take the little trigger wire off the solenoid (slides on). touch it to the battery side of the solenoid. if car turns over (wont start unless you have the key on): put a test light on the little trigger wire. have someone turn the key to crank and watch for 12 volts at the test light. if you have 12 volts, that suggests the solenoid is bad. try jumping across the two big lugs on the solenoid. if it starts, bad solenoid.
if it does not start while jumping lugs, check battery condition, cables and grounds. a jumper battery can help with diagnostics (like jump starting a car).
if you dont get 12 volts at the trigger wire, the problem is in the ignition switch, the wiring from the switch to the solenoid, or the neutral safety switch. with your swap, i dont even know if you have the clutch safety switch - if you do, it is the first thing of the 2 i just listed that i would try).
good luck.