I shorted the connector under the passenger side glove compartment and saw that the check engine indicator blinked 9 times consecutively. I was wondering how to go about this issue. Last week I changed my motor oil and my transmission fluid (I changed the transmission fluid, drove it a couple hundered miles, then drained it and put new fluid in. DEXIII).

The car starts fine, the gears shift smoothly in traffic, however when I start the car and throw into D4 or reverse it searches for the gear and roughly slams it into place . My car occasionally searches for 3rd or 4th while I'm cruising at low speeds.

This probably comes with the territory of the code 9 and I ask for assistance in what to do to get rid of this code for good and for my car to run as smoothly as it should.

 

Just to clarify, was it the CEL(ECU) light that blinked code 9 or was it the D4(TCU) that blinked code 9?

From the description it almost sounds as though this may be a TCU code 9 issue, which is related to the NC/NM sensors...

Two things of note, if the sensors check out its still a good idea to pull them both and make sure they are clear of debris.
Being magnets they attract ferrous material that can build up on the sensor ends and you may begin to lose resolution. This often shows up as random loss or no lockup of converter along with rough or erratic shifting.
When replacing make sure to REPLACE the O rings, once they are disturbed they will not reseal, and will cause for an annoying transmission leak that will cause more shifting issues later.

O rings are part# 91309-PX4-003 (16X2.1) (NOK). They are about two bucks a piece.

If it is the CEL(ECU) light then IIRC that is a crank or cylinder sensor, which IIRC is all in the distributor. Check out the H4A link in my sig for DIY troubleshooting from Tasauto.