Reddit reviews Read and write Hindi script (Teach Yourself)
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Teach Yourself Books
Just looking at images of the Nepali alphabet, it appears to be the same as that used for Hindi. As you may expect though, it will be used in slightly different ways, like the latin alphabet for European languages. I'm learning Hindi and to learn the alphabet I basically just memorized it by writing out each letter and pronouncing it 5 at a time.
You could use Richard Snell's Read and Write Hindi script if you like (https://www.amazon.ca/write-Hindi-script-Rupert-Snell/dp/1444103911/ref=sr_1_1?ie=UTF8&qid=1495039659) but I think you'd do fine using the various web resources available through google, like this one: http://www.omniglot.com/writing/nepali.htm
Of course, real practice comes with exposure to words after you've memorized, so I suggest getting into the actual course as soon as you can. For the first while you'll be doing lots of cross-referencing but that goes away with time and effort.
I am also a Hindi learner and not a native speaker, but I can try to answer your questions.
ऋ is a vowel which can be transliterated as ri or r with a dot below it. It is used in words like कृष्णा (Krishna). You can see that the word Krishna also uses ष (sh) and ण (n). These letters are somewhat uncommon but you still see them, especially in names and Sanskrit loan words. ङ and ञ are less common than ष and ण in my opinion.
ळ is not used in Hindi. It is used in Marathi though. I think it might be a retroflex L. You don't need to know this for Hindi. ऩ ऱ य़ do not exist in Hindi as far as I know. Seems like you already know that some letters do have an added dot(?) to give it a different sound ( क़ ख़ ग़ ज़ फ़ ढ़ ). न र य are not such letters from what I understand.
ॻ ॼ ॾ ॿ - I have never seen these characters with the line beneath them. Either they are old forms or something else. I wouldn't worry about them.
My suggestion is to get some other learning resources. Read and Write Hindi Script is a useful book. I also liked Elementary Hindi and the accompanying workbook.
https://www.youtube.com/watch?v=JMjtkHI7CKM
https://www.amazon.com/write-Hindi-script-Teach-Yourself/dp/1444103911/
https://www.amazon.com/Crash-Course-Learn-Devanagari-Script/dp/1484015118/