Dear Andrew,
as you say, the Unicode representations of upadhmānīya and jihvāmūlīya are not combining characters. As far as I know we have to live with that, so if by implementing them correctly you mean combining with the next akṣara, then I don't think it can be done in a Unicode environment. If all you need is _some_ acceptable rendition, then Tiro Devanagari Sanskrit may be a good font choice. Here's a page that tells you which fonts include these characters and how they look:
As to retaining them in your edition, I'm sure you've already considered that a combining upadhmānīya/jihvāmūlīya can give rise to corruption/variants different from those that might arise from a visarga. So even if the Devanagari rendition is non-combining, using these characters in the edition can indicate to the end user that the Śāradā does not have a visarga here, and that may be helpful.
Dan