My first thought, too.

 

to test the ground, just run a booster/jumper cable from - to the engine, cant get a better ground than that.

 

A 2003 with an original 4.6 ????? really ???

 

OK we are going to assume all was in good operation before replacement took place but with some reservations.

As pointed out and mentioned by me the primary circuit integrity is the first thing to look for. That includes grounds as mentioned by other contributors.
With a Pro Mechanic helping you, the rule of thumb when you suspect a grounding issue is to obviously check that all grounds have been re-installed correctly. If in doubt you introduce a test ground from engine to chassis, (as mentioned )alternator case to battery negative/ground, body to chassis, chassis to battery ground, and ultimately PCM metal case to a good known ground. Correct these issues and you most likely will correct the M&S illumination /falsh activity.

The PCM is mechanics talk for what you call a computer! Specifically the Powertrain Control Module is what you have had presumably re-flashed at some time in the past.
For it to work correctly the line voltages must be consistent and parasitic draws particularly direct to ground must be eliminated.

The next thing is to lift the underhood fuse box cover and check fuses and relays feeding the PCM circuits. Indeed it doesn't hurt to lift the fuse box and see if the harness hasn't been "pulled" in the in change activity. The same goes for the harness running from PCM to the 02 sensors, crank sensor etc, behind the heads. Both can get damaged in advertantly at socket connectors during a change out.
The inability to access the PCM and other modules is of concern; the MIL connector is mechanics talk for the diagnostic connector. It has contact pins designated for various activities and communication with the modules in the car and other functions. It is essential it has good grounds and feeds to excite the diagnostic tool you are inserting into the connector.
Here's a pin out.
Vehicle OBD II Compatibility
Check to see if you have power and good grounds as refered to in the diagrams.

As a matter of point NEVER disconnect the diagnostic tool when in the middle of a diagnostic scan it can leave any on board module in "la la land" with no communication.

My last comment is that using a good scan tool as a professional will ease repair times. I use an Autologic and a Snappy Verus Pro to access all the modes which a simple scanner won't do. I was hoping your Pro mechanic helper would have access to scan and osciloscope functions as in the Verus tool which helps enormously to identify faults. Modes 9 and 10 will access PCM functiocs and see if the operative who re-flashed the PCM did it right as sometimes even the loss of a few Vin digits can cause the program to drop out when powered down as might have been the case when you changed out the engine.

In the meantime I think your best bet is to go over what you have installed and check ALL your connections and correct that parasitic draw.
Usually in this business its the simple things that cause most of the problems.
Take care and keep us posted on your progression.
T/V

 

The best way to test the engine ground, is with a multimeter. Select DC volts, and measure between the engine and the body. Get someone to turn over the starter motor, and watch the reading. Anything above 1/2 volt would indicate a resistive connection somewhere.

My Triumph TR8 (Rover 3.5) had 2 volts between the engine and the body when the engine was running! Meaning the alternator was putting out 14V, but the battery wasn't being charged at all. Had a very bad ground strap. Got a brand new one made.

If you have a resistive connection, the voltage across it will be proportional to the current. That's why I suggested measuring while cranking, this is the highest current case.

 

Don't worry about the grounds right now. It starts, so you have a connection between the BCU and the ECM. So you should have comms on the Diagnostic plug. Alot of scan tools wont connect if they don't get power at the connector. Check fuse 20 under the hood to see if something got messed up and popped it. You need to first get a scan tool to connect to the ECU before you start poking and prodding at things. Don't worry about anything but getting a scan tool to work, otherwise you are wasting time.

 

What lift would you have to have to tuck some 35 inch mud tires.?

 

Ok update here, grounding strap is secure and was tested. all grounds have been tested and have come out to my knowledge as good. What is believed currently is that when the engine was re-installed that a positive wire got grounded out somewhere. Either pinched, or burnt and fused to another wire causing the short. Mechanic is going wire from wire checking.
Believe we are going to try and run a parallel wire to bypass the short to narrow down which one. Any opinions? thanks again for the feedback