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A P0740 is a code for a torque converter clutch problem. This is either the torque converter itself or the control part of the TCC system. Honda's have an issue with transmissions of this generation and in most cases when the code P0740 sets, the transmission will need to be replaced.
I have experienced in the past Civics of this generation taking up to 3 weeks to run it's monitors. My best advise is to drive the vehicle as much as possible under varying conditions to try to get the monitors to set. Once that happens if there are no MIL (malfunction indicator lamp) issues the car will be able to be smogged.
On Passports there is an issue where a wire harness that runs along the suspension will break due to fatigue. When this happens the anti-lock brake light flashes. As I recall the harness runs along the left side of the vehicle. Honda has put out a bulletin for this problem and the repair is to replace the harness with a new updated piece. You will have to check to see if the harness is still available from the dealer. The best way to check this is to do a visual inspection of the ABS wire harness. Start at the rear differential and follow it along the body to the suspension. As I recall the break in the harness usually happens at the pivot point at the trailing arm. There should be a connector there that attaches to the rest of the ABS harness. If you peel back the plastic cover near the connector you should be able to see either frayed or broken wires. If you find this then the repair will be to replace it with the updated harness from Honda if it's still available.
It's always difficult to diagnose these types of issues without the vehicle present. I have experienced this year and model issue before where the transmission will shift into a lower gear for no reason. It did take some time to duplicate the problem though. When this happened the RPM's went up and the transmission had a harsh shift as you explain. In my case the vehicle needed a transmission replacement. My question to you is if this issue is consistant, or happens only once in a while? If the dealer cannot duplicate the complaint I can see how they would not want to sell you an expensive transmission when they have no proof that there is an issue. My suggestion is to try to pin point when the vehicle acts up and note all the details (RPM, engine temp, outside temp, vehicle speed, throttle position) and if possible duplicate it for the technician. This would be a great help in the diagnosis of the problem. Once the technician can duplicate the problem the vehicle can be diagnosed properly and you can get your vehicle repaired.
Engine misfire codes can be caused by different issues other than ignition coils. The misfires will cause a rough running engine, but not cause it to die as a general rule unless there are multiple misfires as the same time. When addressing misfire concerns the engine mechanical (valve adjustment, engine compression), fuel (injectors, FI control and fuel pressure), and spark (spark controls and spark plugs) need to be looked at. If the ignition recall was done in 2002 there is a possibility that there is an issue with the ignition switch. Specifically what you will be looking for as far as dash lights are the engine oil light and the check engine light illuminated. These lights can be seen in daylight. If these lights are not illuminated when the engine stalls I would take a close look at the ignition switch.
This model does not have a throttle cable, it's controlled by the computer. There are sensors on the transmission that the computer reads and determines when to shift. If it shifts hard it could be from a sensor not reading correctly or not reading at all. A qualified technician with a scanner can isolate any sensors that aren't reading correctly.
There are a couple of issues that could be causing this. Look to see if the dash lights are on when the car dies. If the dash lights go out when the car dies then it could be a bad ignition switch. Wiggle the key in the switch after it stalls and see if the lights come back on. If so then that could be the issue. The second issue might be a main relay. There is really no way to test this until the vehicle dies and a qualified technician should check it out for you to see if it's a problem. The main relay sends power to the fuel pump, and if the contacts are bad sometimes power goes away and can cause the engine to stall. The main relay also powers the vehicles immobilizer system so sometimes when the engine stalls the green key light on the dash will flash and that could be an indication of a failing main relay. Of course it's best to have a qualified technician look at these issues for you. Keep notes to tell the techs that work on your car what exactly is going on to help them diagnose it.
It's not the easiest thing to do, but you can gain access either by reaching through from the engine compartment, or in some instances it's easier to get to it by going through the inner fender panel. Some dealerships have a policy that if you purchase a bulb from them they will install it at no charge. You may want to contact your local dealership to see if they offer this service for their customers.
One of the biggest problems with noises is that you can hear them, but can't see them. That makes them particularly difficult to diagnose. It most likely is not the strut bearing or wheel bearing as these usually don't squeak when the vehicle is not moving. Since the noise is coming from the right side I would look at the right side suspension components. The noise can be from dry bushings, worn bushings, loose suspension bolts or worn suspension components along with other issues that are unforeseen. A good visual inspection is a great place to start. I like to put a wrench on all the suspension nuts and bolts to make sure that everything is tight. I also look for traces of rust around bolts as that can be an indication that there is an issue. There is a special tool called a "Chassis Ear" that can help narrow the possibilities down to a certain area. Depending upon your skill level it may be cost effective to take it to a qualified technician for diagnosis.
To get to the EGR passage on a 4 cylinder Accord you have to remove the top portion of the intake manifold. Since this is a labor intensive procedure I recommend that the problem be diagnosed by a qualified technician before any repairs are made. There are many components to the EGR system and each individual part, if not working correctly could cause the check engine light to illuminate with an insufficient EGR flow code. Properly pinpointing the cause of the problem can save you time and money overall.