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You are basically doing what is in the second picture at your link.  You have burned the bootloader and are now trying to run a sketch.  The additional caps are fine.

What exactly is your error?  Are you getting an error message loading the sketch or is the problem that the "L" LED does not light up.

In your first post, you said the "L" LED does not light.  It won't.  If you are trying to run the "blink" program using the "L" led, you are not driving the LED.  You will have to connect an additional wire to drive the LED.  To do this, connect a wire from the mini-uino pin D13 to the uno pin labeled 13.  If the sketch is loaded correctly, the "L" led should blink. 
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The IDE says "Problem uploading to board".
I would expect the L,TX,RX to act the same with both chips when uploading?
What is the L LED?  I don't know, just that it blinks with original chip installed.
Reading... Ah I understand it should not blink. But TX should?
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Yes, TX should blink but on the 5 wire setup you have, the "L" LED will not light or blink.

The last thing would be to take a picture of the back of the board where you have the capacitors soldered.  Then post it here.
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NOT the Uno only refers to the bootoading part.
The extra caps you have are power supply decoupling, Aref decoupling, and the DTR cap, which you are bypassing and connecting to Reset directly.

Once the bootloader is on the chip, the middle section should work the same:

"Uploading Using an Arduino Board

Once your ATmega328p has the Arduino bootloader on it, you can upload programs to it using the USB-to-serial convertor (FTDI chip) on an Arduino board.
[Or with an Uno, the ATMega8U2 performing as the USB-to-serial convertor  - RWP]
To do, you remove the microcontroller from the Arduino board so the FTDI chip can talk to the microcontroller on the breadboard instead. The diagram at right shows how to connect the RX and TX lines from the Arduino board to the ATmega on the breadboard. To program the microcontroller, select "Arduino Duemilanove or Nano w/ ATmega328" from the the Tools > Board menu (or "ATmega328 on a breadboard (8 MHz internal clock)" if you're using the minimal configuration described below). Then upload as usual. "

Connect +5s, GNDs, Reset, and DO to D0, D1 to D1
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Designing & building electrical circuits for over 25 years. Check out the ATMega1284P based Bobuino and other '328P & '1284P creations & offerings at  www.crossroadsfencing.com/BobuinoRev17.
Arduino for Teens available at Amazon.com.

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Found a bad solder joint which sometimes works, especially when you press on it to test it!
The TX pin...

It's all good now!  Thanks everyone!
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Woo hoo! Good news  smiley-grin
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Designing & building electrical circuits for over 25 years. Check out the ATMega1284P based Bobuino and other '328P & '1284P creations & offerings at  www.crossroadsfencing.com/BobuinoRev17.
Arduino for Teens available at Amazon.com.

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