Just leave it with the marks aligned, it should start. I'm going to throw in the IP wiring directions since you've taken everything off.
Ok, here's what you need to do. Turn on key to 'run' position. Check the main wire that comes from the loom to the IP (injection pump), does it have juice. The wire runs to the FSS (fuel shutoff switch) connector first, then to one side of the 'two-prong sensor', When the engine is cold 'juice' will pass thru the sensor, if the sensor is good, and go to either the FIS (fast idle solenoid) or the CTA (cold timing advance), then to the other. If the engine is cold and sensor is good it will be 'closed' and allow 'juice' to get to the FIS plunger which holds the idle speed up. If FIS plunger is working, but not pushing up far enough, use a 1/4" wrench to turn/extend it until the idle speed is ~1000 rpm. The CTA (cold timing advance) near the spider/distribution end of the IP 'advances the timing' to make engine run smoother/run cleaner/less smoke. The 'two-prong sensor' opens/shuts off the electricity to the FIS and CTA after engine reaches 112 degrees, and engine speed/rpm will/should drop to ~650 rpm. If these three items are working correctly, when you go to start engine, hold the throttle pedal at least 1/2 way to floor to allow the FIS plunger to 'set' itself. Use a test light to check for electricity/juice at each of the solenoids, FSS, FIS and CTA. Let me know if this helps. Good luck, Baja