Starting problems on 94 Explorer

[slace22]

Back in October of last year my 94 Explorer transmission went out , it had M5R1 5speed manual...... anyway i didnt have time to fix it right away so it has been sitting up for awhile now.
I just got the new transmission in the other day with A LOT of help from people on this message board in telling me how to do it , i want to say thanks for that.

Before i had the transmission problem i never had any kind of engine issues at all, i ran perfect all the time .
Now that the new transmission is in it will sometimes crank but most of the time it will only turn over ........ but when it does crank it runs good , then i shut it off and it wont start again for a few days .

I am looking for any advice on things to check.
Here is all that has happened while it sat up for months so that maybe it will give you guys some clue as to what is going on.

The only things that i could see as possible issues are...... i left the hood up once while gone all day and of course it stormed but that was months ago.
Also i broke one of the wires going to a sensor on the headers, i repaired the wire.
Other than that there is nothing else that i can think of that i might have damaged while putting in the new transmission.
Oh it has fire and the fuel pump is pumping great , i checked the pressure.
Also the check engine light was never on before but now when it does actually start the check engine light stays on and when i try to get the codes by just turning the key on the check engine light stays on .

Does anyone have any ideas???

p.s. When it did fire up the last time i took it down the road and it ran fine and the new transmission seem to be good, so thanks for all the help you guys gave me on installing the transmission.
But like i said as soon as i got home and shut it off it would not start again for about 3 days.

 

[2stroke]

You are using the paperclip method to check codes right?

 

[slace22]

yes

 

[Watchman]

You mentioned you were using paperclip method. When I first went to check codes I used a short piece of wire to jumper between the two harnesses as outlined in the forum here (How to pull trouble codes...). However, when I went to turn the key on, the CEL came on also. It took me a couple of minutes to figure out the wire ends were not pushed completely into the harness connectors - Then when I turned on the key, the CEL did NOT come on and then I heard the fuel pump activate, then a quick flash of the CEL, then the codes came.

Please try checking your connection of the jumper - using paperclip or wire and make sure its getting contact inside the the two harness connectors. Try using the wire as Doonze suggests - it stays connected better.