Thanks Mellis! Sorry forgot to attached the Eagle files. but here it is.
http://www.sendspace.com/file/6s8mq0
The clearance of trace between the leads of C5, C8 (Vin Trace) is very fine, I have to score it since when I did the toner transfer, it somehow merged with the pads of C5. 
It is also true with DB9 pin 4. I will have to make some modification to this.
Yes, it is working, I have tried uploading sketches to it and it worked fine, also the autoreset worked. I also uploaded the bootloader using the ICSP pins on the board, but have to desolder LED L (on pin 13) first.
I am currently running a sketch on it making it as a thermometer using LM35 with output routed to a 3310 LCD (PCD8544). 