I discovered the problem with bootloading using the newer version of AVRdude. It was actually a hardware issue, but by chance I had only noticed the problem when using the newer AVRdude version: but the problem was there all along. The problem was that I had both the FTDI cable and the Control Head connected to the Digital Interface board's serial port. That is not allowed. Having the RXD lines of two devices connected together is OK, but connecting two or more TXD lines causes problems because both devices attempt to drive the same line. The problem is easily solved by AND-gating together any TXD lines going to a single RXD port.
So bootloading is working properly now, and the latest AVRdude software does automatically reset the processor provided that the FTDI cable's RTS line is connected to the processor's RESET line by a 0.1uF capacitor.
A simple command interface is now in place to allow the receiver to be controlled via a dumb terminal (PC). Just connect the FTDI cable between the PC and receiver, start the terminal emulator program (PuTTY, and Arduino IDE's Serial Monitor both work just fine), and press the Enter key. The receiver will respond with the RDP> prompt. A short session is shown below. Pressing Return, or entering an illegal command, causes the receiver to print out a list of valid commands.
*** ARDF Dual-Band Receiver Ver. 0.3 ***
TIM [hh:mm:ss] - RTC Time
VOL <M:T> [0-100] - Main/Tone Vol
Commands with no data cause the receiver to return the current setting. Commands with data cause settings to be changed. Currently you can control the frequency, band, memories, volume, real-time clock, and read the signal strength and battery levels. We can add more commands as needed. Backspace is supported for correcting typing errors.
This functionality should now allow us to control the receiver (and transmitter too) via WiFi using a wireless TCP-to-UART converter. If you've heard of
Piglet, that is an example of a wireless TCP-to-UART converter. Piglet costs $100 and is a bit of a power hog. But it appears that we could add the same WiFi capabilities using this device:
https://www.digikey.com/products/en?keywords=RN1810-I%2FRM100-ND, which is much less expensive and less piggish with power.
The real beauty of having WiFi support, I think, won't be using your PC to wirelessly control your receiver or transmitter, but using your smartphone! There are apps available right now for both Android and iPhone that turn your phone into a "dumb TCP terminal" capable of sending serial text over WiFi to a TCP endpoint. So there will be no need to lug a laptop out to the forest; if you need to configure a transmitter or receiver you'll be able to use your smartphone or tablet. A specialized app could be written to make configuring and synchronizing transmitters and receivers very simple and portable. Cloning should also be possible over WiFi, eliminating the need for cables and connectors. Perhaps a "Control Head" app could be written to replace the user interface for the receiver - that approach might eliminate the need for a Control Head altogether.
I've got a Piglet in my possession, and I may try hooking it up just to demonstrate the concept.