Welcome to the Doom9 forums, Polar.
Unfortunately, currently BD3D2MK3D doesn't support frame sequential packing. It supports only the Side By Side or Top And Bottom packing methods. However, it is possible to create SBS or T&B files in 720p and full resolution.
I don't own Plex or a DLP projector, and therefore I don't know if Plex can split the two frames and send them as frame sequentail to the projector. You will have to try.
Anyway, all settings related to the resolution of the video are in the last tab. To do full-SBS in 720p, you should select "Side by Side", untick the "Full" option and tick the "Resize video to 720p". That settings are the closest of what you need, but the player or the monitor must be able to split the SBS image to two views.
Also, note that due to a limitation in the VobSub and BD SUP subtitle formats, you cannot have real 3D-subtitles (with the right depth) when using Full-SBS or Full-T&B. You can however hardcode the subtitles on the video stream when you encode the video, and they will be in 3D with the right depth.
Sorry if that doesn't help you much, but I have been unable to find the 3D characteristics of your hardware on the net.
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