I found the hood company on the web www.autohoods.co.uk
I can't testify to the quality of work but having asked them they said the window repair will be indistinguishable from new. I will remove the rear screen myself and post it off to them. They have quoted £95 to repair and return. I think it was about £150 for them to do the repair (inc fitting) but I would have to travel there. They also supply the various parts of the hood itself and the prices look reasonable.
I had a tinker with the hood fluid over the weekend. Drained the greenish kind of liquid in there (?) and replaced with a Dexron IID spec oil. This seems to be the grade referred to in the manual. I achieved very little in the process but I've more tweaking to do.
What appeared to be happening is that when I activated the pump it would very slowly pump fluid out of the reservoir but with not enough pressure to work the rams. The pump (or motor at any rate) was spinning furiously. I am not certain whether or not the fault is that there is air in the pump chamber somehow that just prevents the pump from "grabbing" the oil or whether the motor is spinning but the pump is not turning nearly as fast as it needs to be. Apparently it is not a system that needs bleeding.
To add a little detail this is roughly how the whole thing works.
You have three pairs of rams. One for the rear cover, one for the rear screen section and one for the hood main section.
The pump supplies fluid under pressure to each of these ram pairs.
On top of the pump you have six solenoid activated valves. A pair of solenoids for each pair of rams. One solenoid activates the "raise" ram direction, the other the "lower" ram direction.
E.g. When the hood is opened the rear screen solenoid opens the "raise" valve and the fluid pumps into the pair of rams for the rear screen pushing it up.
The rams are two directional and as fluid is pushed in, extending the ram, the fluid from the other side of the ram pours back into the reservoir. The "lower" operation is achieved by pump fluid into the other side of the ram forcing it closed.
When the motion is complete the next sequence occurs.
There are electrical switches on one of each pair of rams (the left I believe). I guess these must relay the position of the ram to the control unit i.e. fully open or fully closed. There is also a sensor that detects when the hood is folded in (a simple switch on the left hand side, and a sensor switch somewhere in the rear screen section assembly that must sense whether the rear screen movement is on track or something. It's like a ball bearing type push switch thing.
I know my system has sound solenoids as when the ignition is on and the hood is "locked" I can move it manually only when I am also holding in the open-close-roof switch. Thus the solenoids opening properly must be allowing the fluid to pass as I haul the roof up or down. Also the seals are sound in the rams and valves as if I don't press the button I can't move anything as the pressure is locked in (all solenoids closed) preventing me.
I have yet to check all the electrical sensors but assuming these are ok I'm beginning to think that I have a fundamental pump problem. If so I will take it apart! Probably not wise but I've nothing to lose really. That's all a bit techy and there is a great deal of minor detail I've omitted but it may help some of you to figure out some otherwise mysterious hood behaviour.
I intend to inspect my sensors and see what I can do next. I also have a fault code stored (LED in centre console blinks ten times on ignition). I'm not sure what this is but it may just be that the system knows the hood operation didn't complete properly. I have cleared it somehow occasionally but I haven't worked out how yet. Maybe it was ehen I performed a full manual open close cycle. The Alfa dealer weren't helpful when I asked if they could read it and tell me what it said. Instead I may get my own diagnostic reader. I have seen one for £80 that works via a PC and that should retrieve the code if I could find the code description on the web somewhere.
Hope some of this helps!