2. I use the Palm. Works for me. I also like the American Morse DCP iambic paddle. I use the DCP with my Hendricks PFR-3. Yes I am a QRP CW rig collector!
3. I have 2A and 1A AGC and ATC fuses in holders terminated in Anderson Power Poles. 1A should work as maximum TX current at 12 volts (don’t exceed 12 Volts) is less than 1A. Consult the on-line LNR user manual for the MTR3B. The PFR-3 manual also has good info. Remember, not high SWR protection built in. Don’t exceed 12 to 12.5 volts. Use a buck regulator or 2 Zener diodes in series to reduce voltage of full charged gel cell battery. This is in the original PFR-3 manual and the MTR-3B manual.
I assume you have sorted your issues out, but let me add my 2 pennies to the questions for benefit of others potentially seeing this thread.
1. The plug is indeed the same as Yaesu in FT817 or VX handheld series – it is 4.0/1.7mm plug
2. Pico Paddle is best as it fits naturally the side of the rig, and moreover the base mounting hole matches exactly the side screw place in your MTR3b. You just need to replace the manufacturer’s screw with a slightly longer one as you add the base of Pico Palm paddle.