After weeks of testing, initial results are in. So far the most comfortable computer desk setup is putting the Velocifire on the table, the Logitech mouse on the keyboard tray, and having a DreamerCar seat cushion + Samsonite back cushion on the computer swivel chair. Desk height is set to 71 for sitting and 102 for standing.
Having the Logitech K380 + keyboard stand on top of the desk also works as an decent alternative for typing. (The Velocifire is too high to use with the keyboard stand.) The kneeling chair has been untouched mainly due to the inconvenience of moving it into place. The DreamerCar seat cushion is iffy; sitting without it might actually improve my posture.
Anyway, while there is noticeable improvement, things are far from perfect. Sitting at my computer desk for long periods of time still makes my neck and shoulders sore. One thing I noticed is that stomach bloating contributes a lot to the discomfort. If I cut out the bloating, it could potentially make life as a software engineer a lot easier.
PS: nothing is certain. I will continue to fiddle around with different setups these upcoming weeks.