Find And Add Multiple Vlookup Values

I have run into serious trouble with a file I am working on. I have 12,000 companies (roughly), and each of them appears in an Excel file multiple times (some 1 time, other 18 times) with a few parameters. The big file (about 90,000 entries) is sorted so it looks like below:

I will illustrate for 2 companies:

Company A 0 200
Company A 0 0
Company B 300 400
Company B 0 50

I need for every company to do a countif for each column on condition
that the value is larger than 0.

In this case I would end up with:

Company A 0 200
Company A 0 0

Countif result 0 1

Company B 300 400
Company B 0 50

Countif result 1 2

However, I need to extend this to the whole 90,000 entries and 12,000 companies and this cannot be done manually. I thought about vlookup but that returns the first entry only, and I have multiple.