95 isuzu rodeo "check trans" light flashes when i accelerate

You need to take your vehicle an have trans fluid changed . What light is flashing ? Trans , check engine etc... Have it checked for codes .

1st learn to read the codes all by self. it's like USA Indian smoke signals. the delay it the end tells you it's a repeat.
most cars repeat forever , 1 code or many. (OBD1 typical)
44 is O2 lean on one engine .

No engine displacement stated, so .. very hard to answer.
for 100% sure discover what engine is in car, no guessing...
all this is in the FSM.
did you read it?
and autozoned is the last place on earth to ask. (clerks)
and this jewel !!
For Passport procedure, refer to ''Isuzu'' Rodeo.
wiki that, it is true.
and has the ISUZU ECU and ways and means.....
and quotes:
1993-95 Rodeo models W/3.2L engine, connect a jumper wire between data link connector terminals 1 and 3.
and
. On 1993-95 Rodeo models W/3.2 engine, the data link is located under the left hand side of the instrument panel. On all models, turn the ignition switch to the On position. At this point, the "Check Engine" light should flash.
all above is 1st hits with google, my lil friend.
and 2nd hit.
http://www.troublecodes.net/isuzu/iszucel/

I don't understand what you mean by starting in drive instead of first. It should not start in any gear other than park and neutral.
as for the lights , you may have blown a fues or have a dead short from the trailer pigtail you used for pulling the boat.

A CODE SCAN CAN STILL BE DONE, SINCE IT RUNS GOOD ITS JUST A SENSOR PROBABLY AN o2 THAT HAS GONE BAD, THE SCAN WILL LET U KNOW. TAKE TO AUTO ZONE THEY CAN SCAN FOR U

NEW ALTERNATOR, not a SECONDHAND ONE

Are there any Isuzu dealers in America anymore? I thought they all left. If you have one still, go to it.

I would change the trans flter, trans fluid, and have the linkage on the trans adjusted.

I would check the connector at the trans or trans module and make sure you dont have any broken motor mounts.

more than likely it would be your torque converter and not your trans
but you could have the overall dreaded problem that your second gear has grinded its self down and thats why you cant get second gear
no vacumes for the 94 straight mechanical and electrical if there was a vacume you would have found it when you dropped the pan it isnt hard to see around the whole trans cause it would be located next to the speedo with a rubber hose 1/4 thick

Your car has a timing belt. What is it doing on deceleration?