I've made a bit of progress recently, I had a good day on it today.
The air box is in with a new filter:


And connected up via the MAF sensor. That's the Toyota air box and VAG MAF sensor.

And this morning I got round to joining the VAG gear linkage cables with the MR2 gear linkage cables.

It's all covered and sealed now too. I few teething problems with plastic melting as I welded

but nothing too difficult to sort. Its by no means perfect, the Toyota gear stick was designed for only three rows of gears (with reverse being behind 5th), and now it has 4 rows (with revers being to the left of 1st gear). The travel of the cables is perfect, it's just takes a little practice to get the one you want (reverse, 1st, 3rd or 5th). I'll be fitting a quiet buzzer to warn when you've selected reverse. I'm pretty happy with it. I think it would be a dis-proportionate amount of work to make it a really slick gear change.
This meant I could drive the car around the driveway for the first time. It was running for about 3 hours, so I was able to test it a bit. Even so it only reached around 78 deg C. B***dy efficient diesels, I wasn't able to see if the cooling fan worked.
Here's a vid
https://www.youtube.com/watch?v=XR9Hp4XzfU8I have found quite a few problems already though

There a clutch travel problem, well a lack of clutch travel. I thought I was getting away with it, push the pedal to the bottom and push it into reverse and there was no noise. But after a while it began to drag a little and grind into reverse gear. I'll try bleeding it again, but I might have to look into an alternative diameter master (Toyota) or slave (VW). I hope there is something that will fit.
Next, when I really loaded up the alternator, lights, fan, heated rear window, I think the belt area began to smoke, I'm not certain as there was a breeze, but I need to look into this a little further.
Mice have eaten part of the boot seal so I'll need to get another.
And there is a clunk when moving off in a different direction (forwards to reverse or vice versa), I think the third engine mount need looking at. As I was leaving I noticed that the exhaust flexi joint coming from the turbo elbow did not look "relaxed" as it did when I first made and fitted it, it seemed to be at a funny angle (not haha funny either!) So I think I might need to re-make or add too the third engine mount.
These fairly major issues put a bit of a downer on things this afternoon, having thought it was pretty much ready for MOT in the morning.
Oh well.
More to come