Re: LPC 2387 with LPC 2368 settings.
I did almost the same thing and is working without problems on both LPC2368 and LPC2387. I have an old Keil uVision that does not support LPC2300. Therefore I have set CPU as LPC2214, but with startup file for LPC2300 and of course a suitable header file.
Maybe you have overwritten the bootloader code. You can try to communicate with the bootloader using a terminal. The protocol is ASCII based and described in the datasheet. That way you can find out exatcly where is the problem. An alternative is to use a serial port monitor.