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Hey let me see if there is a way I can help... Do you have more details on the DTC'S present and maybe a little more information you can provide on what test you have ran to get it checked up?
I would definitely get that cap on just incase it has anything to do with your starting problem. I will also do some research to get you some better information on that.
If you are able to pull codes it means that some functions of the ECU are operating and mostly your communication lines. Do you still have the new ECU installed or did you put the old one back when it made no difference? Also because it happened after the transmission replacement I would follow the possibility of something being undone rather than something else happened to go wrong. I would prefer to put the old ECU in if possible.
Okay so lets see what we can figure out with that... Those codes are related to both the mass air flow sensor and ignition coils. So when you start your engine I am assuming it just cranks.
Can you check to see if you have any fuel pressure when you crank the engine? You said that sometimes you can hear the pump come on but you need to know that we have pressure. If you don't have a gauge then you can disconnect the fuel line and see if you have fuel coming out as you crank( be careful as fuel may spill out).
Okay if you are filling up a bottle I am sure it is in good condition. Now what about the IG2 fuse and the IG2 relay? Those two are very important for your spark and injector operation...
Okay so knowing that those fuses have power it gives us a good Idea of what of what our next step is. In my opinion there are a couple sure options. It is possible that the components themselves are faulty, which I doubt because the DTC's are pointing to ignition coils, mass air flow and IAC valve. Next there could have been an a short in the related circuits during the repair that may cause a lack of power to those circuits. Finally I think the most possible is the wire harness got stretched during the Transmission removal and is causing the problem to occur. We will need to inspect individual wires from ECU to component and take it step by step.
Okay if it fits loose you would have to check the tabs on the actual fuse box. That is also another strong possibility. That is why checking for power wire by wire to the actual component is a good next step. You can determine if there is actual voltage to it. You may have to find a way to pinch those tabs in so you can insure that both fuse tabs are getting good contact.