The other day I changed the transmission in my 94 Civic DX auto and after the job was done the car refused to start, called it a night and came back the next day with a new main relay and installed it.
Car still wouldn't start, just turns over, as I turned the key over I would get a slight clicking sound under the dash as it did the night before which is why I thought it was the main relay.

About 25-35 min later the car started out of nowhere and kept starting throughout the day about 8-10 times... then while I returned home because the transmission seemed low on fluid, I filled it up and got back into the car and once again back to it just cranking with the clicking noise under the dash.

Checklist:
Distributor checked and is okay spark's and all.
Plugs and spark plugs checked, all checked out okay.
All grounds checked and tested, all checked out okay.
checked for fuel, engine is getting fuel and primes.
checked the shift linkage cable and adjusted it but still no start.
attempted starting the car in neutral and park, still no start.

While I was looking in my Haynes manual I found that if the car attempts to start in anything but park or neutral that the "Neutral safety switch" is malfunctioning, but it did also say this if the shift cable is out of adjustment but I already checked it and it check's out just fine so hopefully this is the answer, I've searched the web for the past 3 days looking for any answer that even comes close to save some $$ but most people are just dealing with a no crank no start situation.

I'll keep everyone posted if the switch works, I would be baffled if it does not.

 

All you did was swap the tranny..? Is the bottom plug on the starter plugged in..?? Not the one that bolts on to the battery, but the one that pushes on..

 

Yeah that's all I did, and yes the plug is in I even pulled and plugged it back in a few times.

I had to rewrite my post to be more informative and to help others find a solution to this situation in the future.
Feel free to re-read my first post.

 

..

 

bumped for new edited first post.

 

If its a crank, no start, you have to be missing the basics such as spark or fuel.

How are you testing for thr above?

 

Tested fuel at the rail and used a test light and other methods to test for spark.

Good news! the car started today and it turns out the safety switch was not the issue.
Even though my brother and I tested all the ground and checked them it turns out the little ground that hooks to the thermostat housing was just barely loose about a 1/4 of a turn or so.. but because it has just enough dirt/grease/oil on the connection it kept it from grounding...
I was like you have to be kidding me...

Once I woke up this morning and thought about your reply Oaken81 from the night before I decided to go outside and scrape my grounds real real good just to rule them out, and ended up finding that one was just a tad loose.

So the lesson here is disconnect and reconnect everything just to make sure.

 

Yeah figures, there so no way a so called safety switch on a tranny would cause you to not start....

 

You probably damaged the trans grounding strap, didn't ground it properly, or forgot it altogether.

Edit: just read your solution post.

 

Nope nothing was forgot. Very basic car. should be completed by the end of next year easily. New suspension and a bit of block work and clean up

 

I can't believe that tiny ground screwed it all up.

Good spot.