I played around with variant forms for E and I today. E is closer to Sanskrit's vowel carrier, and I started from E's 'wave' over the Sanskrit /I/, adjusted to account for Baybayin 'style'. It ended up using the /YA/ character, which makes some sense to me. It's potentially a win-win. It also makes me wonder if /YA/ is distantly related to Sanskrit /I/.
I also thought about an /R/ based partly on the form borrowed from Bugis by Paul Verzosa, and partly on the Bisaya Hervas font's character for D/R.
I think it could work nicely.