Wash the sections with PBS twice for 5 min each time.
I would say that this sentence is fine because of the use of "for." It could be written as follows, and in this example a comma is required:
For 5 minutes each time, wash the sections twice with PBS.
As for your other sentences, I'd say that they are just poorly-written. However, in terse writing there aren't really any rules to be followed – what is written is (close to) the minimum required for understanding. The most common example of this is probably Headlinese:
- Forms of the verb "to be" are omitted.
- Articles are usually omitted.
- Most verbs are simple present tense.
- The future is expressed as "to" followed by a verb.
- In the US (but not the UK), conjunctions are replaced by a comma.
- A long word is sometimes replaced by a shorter word with not quite the same meaning.
- Country names are often used instead of their adjective form.
If I wasn't writing them tersely, I would probably write the sentences in your question as:
Wash the slides with PBS three more times for 5 minutes each time.
Add Strepavididn HRP for one hour, then wash with PBS three times for 5 minutes each time, and then wash with deionized water for 2 minutes.
Wash with PEM twice for 5 minutes each time.