[susan53]

1. I prefer later - but would really change the whole thing. Either :

In the first three months after the company opened, it sold over three million units.
The company opened in June 2015. Three months later it had already sold over three million units.

or

In the first three months since the company opened, it has sold over three million units.
The company opened thre months ago and has already sold over three million units.

(2) is definitely wrong. It must be "since" (ie from then till now) as above.

In the first three months since its inception, the new computer company has sold over three million units.

if you want to use after then the time must be past and the verb changes.
In the first three months after its inception, the new computer company sold over three million units.