I noticed that my right forearm gets fatigued pretty fast practicing Colemak. I can't tell if this is because I'm just not used to the layout yet so my fingers are just tensing up, my fingers are resting on the home row more often (coming from a relaxed "jio;" positioning), or it is because I'm using keybr.com to practice and I'm still stuck practicing mostly the homerow keys.
I dare say it's a matter of practice—you're getting used to completely new motions and balance—and indeed, it might be the case, that your hand posture is quite forced (I remember seeing of my classmates _curling_ his fingers on the home row very unnaturally, for example). Perhaps it'd help you to float your hands more, if you don't do that already.
I also normally use my right thumb to press the spacebar, but I noticed that Colemak uses the right side a lot more compared to QWERTY. Should I try switching over to my left thumb as I learn?
DSK, for example, favors the right hand even more, and many of its users advocate using the left thumb for spacebar, but I don't think that line of reasoning is necessarily valid.
In part because thumbs are relatively independent on the other digits.
In part because keyboards historically often had large and stiff spacebars, and users were encouraged to strike these with both thumbs… It's a waste, though, if you can have a split spacebar—or better, thumb clusters.
I heard that the rolls that Colemak prefers tends to break typing rhythm? (…) I would think the only reason it breaks rhythm is because the brain is not used to Colemak enough to parse the next chain of letters as fast as the finger roll.
L. Malt (the designer of Maltron layouts, basically the first case of the preference for using adjacent fingers) claims, that it's breaking the "rhythm" that makes expert typists so fast, but I guess it's a matter of understanding what the rhythm actually is.
Its probably unfair for me to compare with only two days of practice.
There you go. Any judgment after only two days is gonna be… not exactly representative.