Connecting Arduino Hardware and a Software- serial output together for midi out?

My musical instrument uses an Arduino uno midi sketch for the control of The “Robertsonics/SparkFun WAV Trigger”. The WAV Trigger supports the MIDI protocol on its serial control port, enabling low-latency, 14-stereo voice poly-phony for creating a basic musical instrument sampler.
The WAV Trigger responds to a small range of midi commands, such as Real-time playback rate control and MIDI Pitch Bend, volume, 16 channels and velocity. (Yes you do send MIDI Note On/Off and CC commands to them)
My instrument has a keyboard that has vibrato implemented for the notes. But also I have other notes that must not be affected by the keyed vibrato notes.
As the Wav player uses Real-time playback rate control to control pitch bend i.e. if I send a midi pitch bend message all playing notes will be affected, The sketch I have written controls the two WAV Trigger boards, with software serial for non vibrato notes and the other using hardware serial for the vibrato keyboard notes.
By replacing the original firmware on Mega8u2/16U2 with dualMocoLUFA firmware, Arduino Uno it acts as USB-MIDI device (Standard Midi Class), which is suitable to build music instruments and devices.
I have thought of your idea of using separate MIDI channels for each Wav board, but as I am using all sixteen channels for different instruments, this would half my available instruments