Engine management and wire harnesses are available from several sources.

You can go with F.A.S.T. which they sell a plug n play harness and uses their ECM which you can tune with a laptop computer. It requires a FAST 90MM throttle body which is mechanical and uses an idle air control valve. It also requires a different coolant temp and intake air temp sensor. Nice set-up for someone who plans on modifying their 3G Hemi. I was tempted to use this set-up but decided not to for several reasons. I do not intend to make the engine radical to keep it comfortable for the wife, besides 450hp is enough for her. I am very well experienced with tuning EFI with a laptop, just do not see us modifying this engine. Another reason is the 6.1L Hemi pistons are very unforgiving if you make a mistake while tuning. Due to the small ring land areas, if you go lean even for a brief moment you will almost instantly burn that piston up.
Another item I did not like is FAST does not look at the knock sensors. So go lean too long or detonate without knowing it is very risky.
On the plus side, since it is a mechanical throttle body, throttle response is faster. You can also connect your detent cable at the throttle body.

You have AEM. Been told by many to stay away. I am not convinced on the AEM .
For the price of an AEM I would go FAST which has a better reputation.
Then you got Direct Connection engine harness with ECM and throttle body. Was not available when I started and seemed very pricey. Again, FAST has a greater reputation.
Supposedly tuneable with a laptop Windows based program.

I decided to go with Squier Auto (Hotwaireauto.com). They make an engine harness to use the existing OE sensors and ECM.
They are the only game in town. If you buy the harness from any place else, you are buying from the middle man. They make a nice wire harness. It includes a fuseblock and relays for the fuel pump, starter and ASD. Those items are mounted inside the car. If you have a specific location you want the ECM mounted, you must measure that location from the firewall hole and tell them.
I am hoping we will one day have what GM LS1 engine owners have, HPtuners and EFI Live tuning software which allows tuning the factory ECM with a laptop computer.

Where Squier Auto fell short in is supplying some sort of info. with the harness.
Information such as the minimum size hole you need in the firewall (1.25”), what exactly the main wires need to be connected to and what inputs they need to see exactly.
They will tell you if you call them but it should be included with the wire harness.
I ran into two issues.
When I was ready to start the car it would only tap the starter when cranking. Tap just like when you are setting points on a distributor.
After going through the service manuals and talking to Pete (autodynamics), the ignition wire is not seeing 12volts during crank BECAUSE our older ignition switches do not supply ignition during crank on the same wire.
I took Pete’s suggestion and wired a relay so it would supply 12volts to ignition during crank.
So ok, now the car cranks and starts but then stalls out. I noticed electric fuel pump prime during cranking but then the fuel pump would quit.
I performed continuity checks between relays and ECM connector to find they installed two wires next to each other backwards. The starter relay control was mixed with the fuel pump relay control. Switched them and now she starts and purrs.
Thankfully I work on these things for a living because it was rather easy to find and correct for me. But for the poor soul who does this on weekends only it would have been hell.
Another item to keep in mind. If you are using an ’07 or newer 6.1 hemi, you will need a crank position sensor from a 2006 or older 5.7 Hemi pn#56028815-AA. The connector on the harness is larger and will not connect. Tony told me they have not been able to acquire the newer 2007 style connector.
Another note, the starter solenoid on the inner fender is no longer used to enable the starter. I use that solenoid as a junction block for power distribution now. The starter cranks from the starter relay in the new engine wire harness.
The Engine Control Module (ECM) can be purchased from Squier Auto but it will have a 5.7 tune which will not take full advantage of the 6.1 power and rev capability. It will have the ant-theft feature disabled so we can operate it in our cars.
I decided to purchase a new ECM and shipped it to B&G Specialists. Dave flashed the ECM to 6.1 specs and spiced up the tune for the headers and a higher rev limiter. They also disabled the anti-theft feature.
I’ve seen there are some hand held tuners being sold which can be used for these enhancements but you will still need to disable the anti-theft feature.
If you purchase a used ECM, you will need the VIN number so the anti-theft feature can be disabled. If you purchase an ECM, make sure it is for a ’04-’06 manual trans Hemi Ram. You will need this for either a manual trans or 727 swap. The Manual trans ECM will not enable the rev limiter.

As for the OE engine harness, it can be re-used with a slight modification.
After removing the unnecessary ignition component wiring (i.e. ballast resistor,coil,ECU), I lengthened the oil pressure sender (grey wire) so it can reach the new location by the oil filter. Interestingly the coolant temp sender reached the new location with no modification. The horn and washer wires also did not require modification. I then placed the modified OE harness in a 3/8” convoluted tubing to protect the wires and routed the harness below the intake manifold.
While the intake manifold was off, I connected both heater pipes with 5/8” heater hose. In Hawaii we do not need heat, so I just bypassed it.