I'm hoping for some feedback on this as I'm at a loss and have been searching a few weeks.

I have a 2003 4Runner Limited with a 4.7 V8 4WD. I have been experiencing the following issues.
Intermittent no start
Intermittent clock reset to 1:00
Occasional key fob inop
Occasional - when unlocking factory alarm sounds, immediately stops, then doors unlock.
Occasional dome lights inop.

Troubleshooting steps
Had battery(Diehard grp31) and alternator tested - both good.
Replaced EFI 10 amp fuse
Pulled and tested all fuses in under hood fuse panel with digital volt meter.

Any input is appreciated or suggestions on further troubleshooting. Due to the inconsistency taking it to a shop would be pointless at this point. My next troubleshooting steps would be to confirm good cables to fuse box and alternator and good grounds. Also, while 4R is running pushing on fuses and moving under hood connections (hope for something to happen).

Since your from Arkansas your truck probably came from Gulf State Toyota. They added the alarm system, it's not factory. Do you have the little red light next to the diff lock switch? And the little pin hood switch by the battery? If you do I would be looking at the control box under the dash on the right side of the steering column. I disconnected mine.

I'm not sure what dealership it came from since I bought it used. I do not have the light nor the pin switch under the hood. Since a picture is worth a thousand words. I appreciate the suggestion.

Gulf States Toyota is a distributor, not a dealer. They added things like floor mats, vin etching on glass, pin stripes, alarms, and paint protector to all 4Runners to boost their profit. All imported Toyotas come into the States through a distributor, except in some markets like California and New York.

Gulf States Toyota Distributors (GST) is the world’s second (out of 2) largest franchised distributor of Toyota vehicles. The 154 dealers in the five states of Arkansas, Louisiana, Mississippi, Oklahoma and Texas account for 13% of Toyota sales in the United States.
Southeast Toyota Distributors, LLC (SET) a subsidiary of JM Family Enterprises, Inc., is the world’s largest independent distributor of Toyota and Scion cars, trucks and vans. With 176 independent Toyota dealers in the five-state region of Alabama, Florida, Georgia, and North and South Carolina, Southeast Toyota sales out-pace Toyota sales in every other part of the U.S.

Since your T4R doesn’t have the add-on alarm, I would start looking at trouble with the ignition immobilizer or the ECM for the doors and key fob. Above my pay grade. I think that is what the red light showing the car with the key on it is indicating.

Look under the dash for aftermarket alarm wiring and get back to us. Not all of them have LED

I would start by checking that none of the fuses have pushed the terminals out of the fuse boxes. You will need to get behind the fuse box and pull on each wire to make sure it did not get pushed out. From there start checking ground wires and grounding points. Especially, body to chassis grounds, ECM to body grounds. I would also look for signs of rodent damage to wiring.

@V8Man @BlackWorksInc @gm350reratliff , Thanks for the info and suggestions.

I checked the dash and didn't see any extra wires or an alarm brain. I did disconnect any extra wiring on the battery to eliminate add-ons (winch,sub amp,compressor).

Last night I had several issues back to back which is odd considering but everything worked fine today.

As I have time I'll start checking grounds but I'm not sure where to start at this point. As for the fuse connections, I confirmed each connection seemed firm when checking the fuses but I will also see about accessing the rear of the fuse panel.

Again thanks for the input and I will update everyone as I have time to proceed. I'm hoping the extra wiring is causing issues and it will be a simple process of elimination.

I'd start at the battery terminals and work my way down each connection point in the engine compartment. Check each terminal for tightness, and maybe more importantly, check each wire connection to the terminals (crimp).

Since you removed the extra wiring from the battery and it then did some back to back stuff, it sounds like you're close to it right there.

@03BlueRunner , you might be correct. So far today I have no issues after disconnecting the extra wiring. I'm going to leave it a couple days and see what happens. Once confirmed good I will add one wire at a time until I determine which causes the issue.

Good luck - I hope you'll lock onto it soon. Those electrical bugs can be a real stress on you. Sometime all you can do is take it one step at a time. I'm in the midst of a similar issue on my wife's MDX. The battery dies at will - I think I have it narrowed to the Bluetooth module (thanks to an MDX forum for the posts!).

Thanks for the post - Im having a similar issue with the exact make/gen. Posted my details in this thread too.

Repost:
Got to the vehicle this morning, fob wouldn't unlock, used key, set off alarm, used fob to turn alarm off. My clock and tripmeter both reset too. This is the 4th time this has happened and speculate there is a wiring issue somewhere. Replacing the "Big 7" cables and hoping this helps somehow.

Looking to solve and not disable too.