Hi!
New here, so apologies if this has been asked before (I searched):
My biggest challenge so far is that I often remember the mnemonic for a reading but don’t remember how that translates into the exact sounds (and thus spelling) of the reading. For instance, remembering that ’input’ (mnemonic “new lock”) reads as にゅうりょく, and not, say, にゅろく or にゅろきゅ. Other than trial and error, any tips for translating a remembered mnemonic into remembered proper pronunciation and spelling?
Don’t be affraid to make up your own mnemonic. It is something you should forget over time anyway. If you keep failing an item, try to remember what was the first thing that popped into your head and try to tie a custom mnemonic to it. Or make a mnemonic that sounds like the thing you want to remember. Or make a picture in your head and remember that. For example remember that ‘new lock’ is close to ‘new rock’ and you have that ‘りょく’ right there.
Fun fact (I assume you went over hiragana lectures at some point and may know this), R and L are almost the same in japanese and are represented by the same kana. The actual pronunciation of the R column kana is somewhere in between, shifting closer to R or L for some words. When writing, always write R, not L. If you try to type ‘LYOKU’ you get different kana output, because L is reserved as a prefix for writing small kana. Try it yourself.
I’ve only ever used mnemonics for readings for the occasional word that I have trouble with, so this is kind of a non-answer to what you’re asking. That said, I find hearing and repeating the audio of the word each review helps in getting this kind of “is it long or short” into my brain better than reading the word alone. Also, at some point you pick up on patterns of what on-yomi are more likely than others (e.g. にゅろきゅ is very unlikely sounding). You also gradually get enough cross reinforcement from other words using the same kanji that you remember the on readings that way, but that does take a while to build up.
I really like the idea of creating a new mnemonic based on the first thing that did come into my mind upon reviewing, thanks!
And yes was aware of the r/l pronunciation 
. My main struggle in that example was remembering the ‘i/y’ sound (りょく instead of ろく), when that sound is not in either ‘lock’ or ‘rock.’ (Though of course now writing this many words on it and I shouldn’t ever forget it…)
Also new here, (and thus recently exposed to the problems you’re facing). I find that it helps to remember the readings of the individual Kanji that compose a word and just smash them together. Sometimes this will burn you if you forget the rendaku or on a word like 下手 (read へた), but for the most part it helps and I imagine that will only work better as my vocabulary expands. This is also encouraged by the fact that WaniKani will only give you vocab that use Kanji you’ve guru’d. If you go back to the mnemonic for 入 it talks about saying “neeeeeeeew” in an announcer voice.