Looking on the internet deeply has found these results:

he had come yesterday is the most popular phrase on the web.

he had came yesterday 10 results on the web	he had come yesterday 1125 results on the web More popular!
Some examples and use cases from the internet:	Some examples and use cases from the internet:
It doesn't look like this phrase is very popular! The search could not find any examples on the internet.	... because I wanted him in my difficult time(I was very close to my grandpa) but he flatly refused to come saying he had come yesterday only. Jul 26, 2012 ... ... bright, fast moving across the mountain sky, headed in the direction from which Anselmo and he had come yesterday. The three passed and ... Jan 22, 2015 ... He had come yesterday to meet the President. At that time, the cabinet meeting was underway. He had requested for an audience with the ... Mar 18, 2014 ... 'I wish he had come yesterday' (James 1982: 384). Iatridou (2000: 243) speculates about the possibility of tracing back constructions like (50) ...

he had came yesterday

10 results on the web

he had come yesterday

1125 results on the web

More popular!

It doesn't look like this phrase is very popular! The search could not find any examples on the internet.

... because I wanted him in my difficult time(I was very close to my grandpa) but he flatly refused to come saying he had come yesterday only.
Jul 26, 2012 ... ... bright, fast
moving across the mountain sky, headed in the direction from which Anselmo and he had come yesterday. The three passed and ...
Jan 22, 2015 ... He had come yesterday to meet the President. At that time, the cabinet meeting was underway. He had requested for an audience with the ...
Mar 18, 2014 ... 'I wish he had come yesterday' (James 1982: 384). Iatridou (2000: 243) speculates about the possibility of tracing back constructions like (50) ...