I would usually use ... to show that I have deleted text from a quote, however, I recently discovered an issue with this when the text ends with a question mark before the ellipsis. So if the quote is 'Why did we go back?...We wanted etc.' So my question is does the question mark act as the first full stop or do you still put in three after the question mark?
A full stop does not act as the first point in the kind of usage you are thinking about, where an editor (i.e. you) has selected from the original text.
Three dots at the end of what looks like a sentence generally conveys some kind of pause (questioning, ironic, whatever) on the part of the original writer, or the thinking/speaking character at that moment (as pointed-out in the MHRA Style Guide: see below).
In academic or other analytical writing, the most common conventional sign for editorial ellipsis includes the use of square brackets. To adapt (slightly) your own example:
‘Why did we go back? [...] We wanted [to do it again].’
In that case, you have made the reader plainly aware that the original writer posed a question, and a little later gave an answer to which you want to progress immediately (and in my amended example you wish also to summarise that).
In this way you dutifully also show that there was intervening text, which you have determined to be too long-winded or distracting for the purposes of the present discussion. You have conscientiously shown readers that such text exists, should they wish to go and hunt it down (assuming that your referencing allows that).
(In my emendation of your example, a second ellipsis again shows that you have removed original text, but in that instance you have replaced it using a briefer or otherwise more useful gloss of your own.)
Returning to the matter of the question mark... It really does not matter how that sentence terminates. You might easily render a very similar quotation as,
‘We asked ourselves why we had gone back. [...] Frankly, we just wanted [to do it again].’
Typographical extensions of this kind of practice can indicate ellipsis of part- or full paragraphs. It is unusual (although not impossible) for this kind of sign to be useful for ellipsis across many pages.
The MHRA Style Guide provides very concise advice (p4):
In quotations, points indicating an ellipsis (i.e. the omission of a portion of the text) should be enclosed within square brackets:
Her enquiries […] were not very favourably answered.
It does not mention sentences, question marks or anything, because they make no difference.
Sections 5.7 and 9.6 in the same document give more detailed examples, but the simple, core principle will help you a lot: ellipsis >> square brackets.
EDIT I should have mentioned... This convention might well last you a painless lifetime, but it runs into an unavoidably inelegant wall if you need to quote, verbatim, a text with square brackets in the original.
I always try to re-select such a quotation to avoid that detail of original usage, because that kind of stylistic interruption takes the reader out of your text. That can be utterly impossible in some cases, however—for example, if you are critiquing another critic’s selective assessment of a text.
If you cannot avoid the original square brackets without losing the necessary sense, then you are stuck either with prefacing the quotation with a note like ‘(ellipsis in original)’, or somehow (e.g. in a prefaratory note, or a footnote) explaining that for the sake of clarity (!) the original square brackets have been replaced by some other kind.
The good news is that very few will ever find this special case to be any kind of problem, in any case. The basic square-brackets convention will serve almost everyone perfectly well indefinitely.
(Quoting quotations can introduce far worse headaches, especially with conventions of easily-conflated single and double quotation marks.)