Assalamu Aleikum
1) I have noticed that the "yaa" and the "alif" are used to lengthen and determine long vowels such as in
However, I have noticed that in the name "Musa" (Moses) in the Quran, for instance in
2) In
Would you please explain whether or not one should read this type of alif or not?
May Allah bless you all inshallah
Answer
Wa alaikum assalaam wa rahmatu Allahi wa barakatuh.
1. The alif maqsooraa is written as a 
with no dots on it, and the addition of the small dagger alif is put in by the scholars to show it is pronounced as an alif, such as in 
, and 
. This alif was, in most cases, originally a and has changed into an alif for grammatical or other reasons. The qira’aat that have imaalah, such as the qira’ah of 
and 
make imaalah of this alif changed from a in a large percentage of the cases. As you may know, imaalah is part alif and part . The alif maqsooraa then is indicative of an alif that has originated from a , and in many cases for some ways of recitation, this alif is read as a mixture of an alif and a .
2. The word 
in aayah 44 of surah Fussilat has a special symbol (i.e. black dot) over the second hamzah, to show it is read a special way in the recitation of Hafs ‘an ‘Aasim. This second hamzah is read with 
, meaning in this word it is read with an “easing” of the hamzah so that it is in between a hamzah and an alif. This is a word that is read different ways in the different qira’aat. Please also see: http://www.abouttajweed.com/that_what_is_needed_for_hafs_part_3.htm
May Allah bless you as well.