1. The Basmalah between two surahs

The recitation of Abu Ja'far always has a basmalah between two consecutive surahs when reading the end of the first surah in continuum with the next consecutive surah.   The exception to this is when joining Al-Anfaal with At-Tawbah, as there is no basmalah at the beginning of surah At-Tawbah. 

2.

The recitation of Abu Ja'far reads in surah Al-Faatihah with no alif.

3. Lengthening of a dhammah on the plural meem on the end of a word.

The recitation of Abu Ja'far reads with the lengthening of a temporary dhammah put on the plural of two vowel counts on the end of a word, if the first pronounced letter of the next word is voweled. Example words can be found in the following aayah:

(Al-An'am 87). 

4.  Lengthenings:

Abu Ja'far reads  with two vowel counts and with four vowel counts.