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On the results of measuring the amount of plastic found in a sample of 31 fish:

その結果、9匹の体の中から大きさ5mm以下のプラスチック平均で1.1個見つかりました。
The result (was that) from 9 fish the size was at least 5mm of plastic but on average they found 1.1mm.

I'm struggling with several aspects of the grammar in this sentence:

1) Is the first が in bold a subject marker and the second が the conjunctive particle? Is there a だった omitted before this が?

2) Is the counter word 個 somehow used as a substitute for repeating the unit mm?

If not, then I'm lost on how to parse this sentence.

5

Both が in this sentence are subject markers.

Consider this "double-subject" sentence (cf. 象は鼻が長い / 私は彼が好きだ):

そのプラスチックは大きさが5mm以下だ。
Those plastic (fragments) are 5 mm or smaller in size.

Form a relative clause from this (note that ~以下 works as a no-adjective):

大きさが5mm以下のプラスチック
the plastic (fragments) which are 5 mm or smaller in size

With this as the subject of the main sentence, you can say:

大きさが5mm以下のプラスチックが見つかりました。
The plastic (fragments) which were 5 mm or smaller in size were found.

個 is a generic counter for small and round objects. 個 is not a pronoun and it never replaces a unit of length, time, etc. So this 1.1個 refers to the number of plastic fragments per fish (cf. リンゴを2個買った). 平均で means "on average".

大きさが5mm以下のプラスチックが平均で1.1個見つかりました。
An average of 1.1 plastic fragments which were 5 mm or smaller in size were found.

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