Have 02 honda rubicon trx 500 D1 D2 esp lights flashing will not shift out of 1st gear and runs really bad in reverse

turn machine key on in N, but hold your shift buttons, both up and down, turn key on and hold for 10 seconds, then it will flash a certain amount of times, go get a service manual, and look in the codes section, it will flash different for each code it is thorwing, kind of like a check engine light, or let me know how many flashes and I can look it up.

do you push the reverse safety button when going in reverse

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The flashing s light means a transmission problem. The transmission computer is under the carpet on passenger side under where you put your feet. Pull down the carpet to see the diagnostic light. Turn on the key to count the flashes to get the code. Pulll a list of codes from the internet.
If your trans shifts properly if you manually shift it thru the gears, going from D1, D2 D3 but feels like it is starting in second when in drive at a stop, the computer is probably the issue, and can be repaired or exchanged for a good computer, lots of companies do this ,find 1 on the internet.

the D lights blink for A/T failures
in the USA (are you) the first check is to scan it.
(and drive it checking for slip,flare or other symptoms)1st !!!
#2
connect the scan tool 0bd2 and scan it for tranny errors)
if you read the FSM , it shows each step in sensor tests.
and lots of not..... (scope readings missing, bad bad bad)
first off , you need some facts:
if the scan tool shows the rear (wild guess) speed sensor reads wrong, do not think its bad, you fail to realize most failures
are the transmission slips (trans, is bad) and the sensor see this illegal
low rpm and trips a DTC for that.
most those sensors last forever,
THe ECU (PCM) never knows what is wrong, it only knows
what tests fail,.
The ecu knows the speed of the engine and the tranny speeds.
this is the TCM function (be it in a TCM box or in the PCM)
this TCM does all the shifting and monitors for errors.
The DTCs in many case should state, tranny slip or bad sensor.
and dont.
you didnt post the DTCs so can elaborate.
working the A/T with no FSM. is not going to work.
you need to read the on car service, and do the steps in the correct order. fiddling a sensor with a tranny with low pump pressure. is folly
so is same and the stall test fail. (1st tests both)
my byline:
"the PCM is dumb. it never knows what part is failed, ever.!!!"
think of DTCs as only clues, or 1 more symptom....

You may have a problem with your IPC (Instrument Panel Cluster) which often can be exchanged for a serviced and warrantied replacement unit.

First thing I would try...disconnect the battery for 10 minutes which will allow the on board computers to re-start.

If this doesn't help... I would retrieve any stored codes the on-board computer has logged which may provide a starting point to diagnose your trouble.

For Automatic transmission problem,click the link below:---- Automatic transmission troubleshooting:----

http://howtobyme.blogspot.com/2011/11/automatic-transmission-will-not-go-into.html

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Automatic transmission shift lever issues?-------

http://technoanswers.blogspot.com/2012/01/automatic-transmission-shift-lever-hard.html

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AUTOMATIC TRANSMISSION FLUID LEVEL? --

http://schematicsdiagram.blogspot.com/2011/07/how-to-check-automatic-transmission.html

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AUTOMATIC TRANSMISSION FLUID AND FILTER?

http://schematicsdiagram.blogspot.com/2011/07/how-to-change-automatic-transmission.html

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Transmission fault light on car dash?

http://schematicsdiagram.blogspot.com/2011/12/transmission-fault-light-on-car-dash.html

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Transmission shifting problem?

http://schematicsdiagram.blogspot.com/2012/01/transmission-shifting-problem-on-toyota.html

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Transmission Slips out of 2nd gear?

http://repairhelpcenter.blogspot.in/2012/02/transmission-slips-out-of-2nd-gear.html

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OD light flashing and transmission fluid leaking?

http://repairhelpcenter.blogspot.in/2012/02/od-light-flashing-and-transmission.html

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Why Transmission fluid leaks near radiator?

http://repairhelpcenter.blogspot.in/2012/02/transmission-fluid-leaks-near-radiator.html

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Transmission fluid leaking?

http://technoanswers.blogspot.in/2012/02/ford-windstar-transmission-fluid.html

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****** wont go in reverse?

http://technoanswers.blogspot.in/2012/02/dodge-neon-wont-go-in-reverse.html

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Automatic transmission will not go into reverse?

http://technoanswers.blogspot.in/2012/02/dodge-automatic-transmission-will-not.html

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Transmission is making buzzing noise?

http://technoanswers.blogspot.in/2012/02/transmission-is-making-buzzing-noise.html

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This will help.

Thanks.

Sounds like a linkage/cable to me. Disconnect the linkage at the transmission and move the shift actuator by hand to see if there is the same things happening. Don't try to do this with the engine running unless someone is holding the brake inside the car.

if you drive the car with the shifter in d1 and while driving down the road move the shifter to up shift the foward gears individually if the rpms drop every time you up shift you know your trans shifted if this allows you to go through all gears you have an ecu problem if the car still doesnt shift you have a trans problem and would need to take the car to a transmission shop

This issue is caused by a transmission fault or malfunction, most likely a shift solenoid in the trans has failed or the trans control module has a problem, the trans can be tested for codes that will show what circuit or component of the trans controls is causing the light to stay blinking, have it tested.