Originally Posted by: RiskyNZOk I've just started trying to improvise over Jazz standards.[/quote]
Good deal! First, I'd encourage you to look at my Intro to Jazz Guitar (if you haven't already studied it):

http://www.guitartricks.com/tutorial.php?input=519

Originally Posted by: RiskyNZI know Autumn Leaves is diatonic, so I could have just played one scale and stressed the root of each chord plus a few other tones - in fact this is something I'm good at already which is why the 2-5-1 improv worked.
[/quote]
Autumn Leaves was originally written in E minor. So, that's the version I'll refer to as I reply. If you are working in a different key, please let me know so I can adjust my replies as necessary.

Regardless of which key you are in, it is important to notice that the tune does modulate from minor to relative major. Look for the accidentals at the endings of the 1st phrase. Also, there is an interesting descending chromatic chord sequence near the end of the form. The melody holds one note throughout it, so it doesn't factor in right away. But it is a great place to work out some neat solo ideas.

Now to your questions!

Originally Posted by: RiskyNZ1. Should I even be trying to visualise a diatonic progression without reference to the parent major scale or is this complexity redundant?[/quote]
The first thing you should do is learn the melody. Learn to play it, learn to hum it, hear it in your mind. The melody is the starting point.

You should start by thinking of this tune as in one key (with slight melodic & harmonic minor modulations) or as you say from one parent scale. It is a sort of redundancy because a diatonic progression that stays (mostly) in one key has only one primary scale (with slight modulations).
[QUOTE=RiskyNZ]If I should be visualising one big major scale and singling out appropriate tones, how do i handle modulations or out of key chords/notes when they crop up?

Combine 2 essential components: The melody & the fact that this song & it's melody use the key/scale of E minor. When the melody contains the modulations raising the 6th & 7th degree then alter your soloing at that point. There are other times in which the B7(b9) to E minor chord happens (V-i progression) but the melody doesn't contains them. You can still use the altered scale notes in these places.
[QUOTE=RiskyNZ]2. Does anyone have a list of good progressions to improvising over, from easy to hard -they can be things on this site or just songs or something that you found helpful to practice improvising over.

Any Real Book is a good place to start. Or here is a site that you can use:

http://www.jazzstandards.com/compositions/index.htm
http://www.realbook.us/

But please note that these sites don't publicly publish the most important part: the melody. That is a great reason to buy yourself a Real Book.

Traditionally, jazz soloing is about playing the melody, then altering it by ornamentation, then using it as a strating point or platform from which to connect the chords of the tune with approach tones. This means that any given chord might be regarded as a the I or i chord of a miniature "localized" ii-V-I/i progression & how the playing achieves this is his individual style.

For example, overall the song is in E minor. But when any given chord comes along, say the C major 7, you regard that chord as it's own localized I chord. One measure before that chord arrives, you play notes that outline or imply Dmin7-G7b9 as a ii-V approaching the C major 7 as a temporary tonic.

It might sound a little "odd" because the actual chord at that point in G major 7. But this is often precisely why jazz sounds as it does: implication of where you are headed, juxaposed with what is actually happening at the time. :)

To learn this sort of this it helps to learn some licks by Charlie Christian, Django Reinhart, Louis Armstrong, Charlie Parker, etc. to hear how this is accomplished. I am currently working on a new Joe Pass tutorial on lead licks so that might help you in the near future. For now, have a look at this tutorial on the Circle of Fifths, in particular starting at lesson 7 apply the idea of secondary dominants to popular songs.

http://www.guitartricks.com/tutorial.php?input=835

You might also get something out of these simpler tutorials that show how to combine major notes in minor pentatonics in a blues context. The idea is to target chord tones, which is great practice for preparing to play jazz changes:

http://www.guitartricks.com/tutorial.php?input=217
http://www.guitartricks.com/tutorial.php?input=232
http://www.guitartricks.com/tutorial.php?input=244
[QUOTE=RiskyNZ]
3. What are the steps to being able to switch between modes fluidly? I have vague ideas of what is important - like fretboard knowledge and scale pattern knowledge, but I'm not sure what order I should approach things in and have hit a rut. Should I be learning licks for each mode - which I have shied away from, or is it possible to just learn the patterns and make your licks as you go?

You need to the physical skills of course. But you also need to know ahead of time what each mode sounds like so you can pull that mode out at will on the spot when you desire that sound. But you can only do this once your physical skills are up to par. So you need to develop your playing & listening skills together.

The next step is to develop your own vocabulary. You should have standard licks, or ways of playing through progressions that you like, that you've developed because you like the sound of them. The bigger your set of pre-established licks is, the more you mix, match, alter, interchange & interconnect all these things.

This tutorial on practicing modes can help you with practicing them in a way that compares & contrasts them in order to learn to hear them better as you are gaining physical skills:

http://www.guitartricks.com/tutorial.php?input=770

Ask more as necessary. Have fun!