I know, that probably there's no Ca'Non for this, but I'll ask anyway.

Should I write:

raSDaq vIghro' tu'lu' 

or 

raSDaq, vIghro' tu'lu' 

Should I write:

pa'Daq vIghro'vaD nIm vIqeng 

or 

pa'Daq, vIghro'vaD nIm vIqeng 

or 

pa'Daq, vIghro'vaD, nIm vIqeng 

Should I write 

vIghro' gha'cher bo'Degh je vIlegh 

or 

vIghro', gha'cher, bo'Degh je vIlegh 

Should I write 

jISop 'ej jItlhutlh 

or 

jISop, 'ej jItlhutlh 

It doesn't matter. It really doesn't. So far as I know, no one has ever written a popularly accepted Klingon style guide of punctuation, and even if someone had, it would be a prescriptive style guide only, not a rule.

That said, here are my suggestions.

I usually reserve commas for separating purpose and subordinate clauses from other clauses if they are complex enough to be potentially confusing, and for separating items in a conjunction of three or more items (and please include an Oxford comma!). I might use one to separate a time expression from what comes after it if it's unclear where the one ends and the next begins. Occasionally I'll use a comma to separate a quotation from a verb of speech, though my approach to the punctuation of this has never settled down. (I am currently not in favor of always using full quotation marks around the quotation.) I tend to use semicolons between closely related sentences that have no verbal link between them (e.g., 'uSDaj chop; chev).

I recommend keeping punctuation to a minimum: use no more than necessary to remove any awkward spots in a text. Don't use it to show verbal pauses. (If you must show verbal pauses, only do so when reporting dialogue, and use an ellipsis.)

-- 
SuStel
http://trimboli.name