I have been asked to translate the following phrase:

'it's where you're going that counts' and wanted to check and see if there were any other suggestions. Now some paraphrasing required given we can't use 'counts'. So far I have come up with:

'Is é an áit a bhfuil tú ag dul is tábhachtaí'

A predicative adjective should always come first in a normal Irish copula sentence:
Is tabhachtaí é an áit a bhfuil tú ag dul. (lit. "Is most important the place where you are going")

But you can use some kind of prolepsis:
An áit a bhfuil tú ag dul, is tabhachtaí é. (lit. "The place where you are going, is most important it")

grma

Should I use 'í' given that 'áit' is feminine? And given it is more of a 'life journey' than an actual destination, what about

Is tábhachtaí í an áit a bhfuil do thriall

?

Yes, the noun áit is feminine. But it is usually referred to by the masculine pronoun é, so most often "é an áit", rarely "í an áit".
triall is okay

I could add this shorter version:
Is é an áit is tabhachtaí (ná) do thriall. (lit.: "It is the place which is most important: your journey")
(In this sentence only é is possible because it is referring to "do thriall")

Having reconsidered it:
Your sentence isn't really wrong grammatically but probably awkward for two reasons:
1) "Is X is tabhachtaí" is a cleft sentence ("It is X which is most important"). But copula clefts are often expressed with a real antecedent: "Is X an rud is tabhachtaí" or "Is X an ní is tabhachtaí"
2) the intervening relative clause "a bhfuil tú ag dul" makes it a bit more strange and calls even more for a noun "an rud" or "an ni" (in my opinion, at least)
So,
Is é an áit a bhfuil tú ag dul an ní is tábhachtaí.