I now produce most of my recordings by converting each midi channel to individual wav files.
I did this video a few years ago to illustrate the process
https://drive.google.com/file/d/1GiYYT9KsK1tv9Bc7pWYp4Gc6pTo-cH11/view?usp=sharingUnless you can find someway of semi-automating the process, it can be a long-winded process; and one of the problems to overcome is (as you have found out) getting all the wav files in sync.
So, my solution is:-
(1) Transfer your midi song recording to PC;
(2) Convert the midi file to Type 1 (you can Use MixMaster to do this, or 'gn1to0' which is a freeware utility from gnmidi.com);
(3) Produce individual 'solo' midi files for each midi channel/track in your Type 1 midi file - 'midimutt' from gnmidi.com can do this, but it is a DOS command line utility (costing 18 Euros), so you need to be familiar with using command line utilities;
(4) Use midi2wav (from midi2wav.com) to record a wav file from each solo midi file. This costs about $30, can do all the files in a batch process and produces perfectly synchronised wav recordings.
Sounds like a lot of messing about, but once you get the routines sorted it can be done quite easily, and the biggest time (recording the wav files) can be left unattended.
I also have a Roland FA08 workstation, and it has the rather unique feature of being able to automatically produce individual wav files for each midi track in midi files recorded on the FA08.
Regards
Roy