You can get an OEM (Valeo) clutch kit for about £160 on Eurocarparts and also I've seen plenty on eBay from various sellers including some alfa specialists such as Autolusso. £550 for changing it seems about right as it's a lot of work!
I'll be doing the work myself as I have the use of a ramp and nice clean workshop to do it in - friends of mine - although as their business is VW/Audi abd BMW tuning I have to take a lot of stick about owning an Alfa!! I just remind them that all of the 'weak' parts prone to failure on an Alfa are generally German made!! (Bosch)
I did change the clutch master cylinder about a year ago and exactly as other people have mentioned the slave failed straight away as well.
When you mention that your clutch is biting very low do you mean at the top of the pedal travel? Mine bites right at the top and when pressing on hard it slips as you change up a gear.
The LSD option is something I've decided to do after reading the posts about people having had their standard diffs let go - the thing is my car has already had a replacement gearbox (judging by the 'Alfa remanufactured' label on it) - so it's made me worry about it enough to go for it - also it will benefit the handling. A Quaife ATB LSD is about £550 to 600 for the kit.
Manifolds... Again I have read and had discussions about these and apparently the standard 'Maniverters' are very restrictive so by effectively removing these cats you release about another 30 hp! We shall see. These manifold catalytic converters are there to heat up quickly and get the emissions down but the centre cats do this fine as well so there shouldn't be any problems with emissions once the car is warmed up. No problems with MCSF errors either as there are no pre-cat lambdas on these cars. Edit: there are pre-cat but no post cat lambdas after the maniverters.
Equal length downpipes should help with the breathing of the engine due to them being the correct lengths for the exhaust gas pulses to converge at the correct point and scavenge the next pulse etc. Exhaust tuning is an art and all I know is that many years ago when I fitted my Alfasud 1.3 TI with ANSA EQ manifolds the difference was unbelievable!
Of course all this extra power only comes about at peak revs etc so there probably won't be much difference for normal driving, and I tend to drive steadily most of the time...
As for independent garages there is only one guy I would trust with my Alfas. He has a small but busy workshop not far from Stroud where I am. He doesn't advertise himself as an Alfa specialist but having owned and worked on Alfa's for years he knows his stuff. Martin at MKG. There are others but I don't have any experience with them so can't comment.
I hope this helps somewhat.