Hello greddin and welcome to these forums. You'll find many helpful people here and a lot of useful information. Make sure that you:
I think I would enable IN Port 1, OUT Port 2 and OUT Port 3. THe MIDI signal path would then be_
-- Roland A-90 to Micro Lite IN 1
-- Micro Lite to computer / Reaper "Micro Lite IN 1"
-- Reaper / computer to "Micro Lite OUT 2 (or 3)"
-- Micro Lite OUT 2 to Roland JD-990
-- Micro Lite OUT 3 to Korg Wavestation
Now, to use these paths in Reaper
-- enable the devices as above
-- select "Micro Lite IN 1" as the MIDI input device for a track
-- select "Micro Lite OUT 2 (or 3)" as the MIDI hardware output for that track
-- set the track for MIDI Recording (or monitoring only) and off you go.
Details of all of these steps can be found in the User Guide. Also, in the MIDI Device Configuration I would give the various ports aliases to show what device is connected on each port.
Let us know if you run into any problems.
PS Your hardware diagram made things much easier to explain. In my version I added numbers to the signal paths to indicate the flow of the MIDI / audio signals through the whole system. Here's the link for other readers:
How to describe your hardware set-up (in Post #3)