By the sounds of it, the GT has probably been standing for a while previously.
Common issues and varied difficulty of cures: cheapest and easiest first
1. Look at the clutch pedal at the top of the arm you will see a cylinder with a metal pin(plunger). Get hold of a spray tin of silicon lubricant (not WD40). Using the straw extension provided, push it gently into the inside edge of the rubber boot seal on the plunger and give it a good squirt while working the pedal with your hand, job done
2. Have you been doing short trips since buying the GT?
Check the fuel filter under the engine cover, there is a plastic drain nut at the bottom, open it gently while holding a jar under to catch the diesel that comes out. Chances are you have water in the fuel system which is normal and needs draining every three month or so..... I have lost count on how many fault screens on JTD's come up because of this simple task not being done often...
A handy tip is to change the fuel filter regularly and you never get any hassle out of them!
The EGR valve is caked in carbon and soot (another sure sign of standing for long periods and short driving trips) do a search for "EGR & MAP sensor" how to clean... Bear in mind taking on an Alfa is not like owning a german car, you have to be a commited owner to doing some basic work to keep them tip top, there are no pretty nagging service lights to let you know what needs doing, its a true driver's car and needs to be respected and worked on accordingly, not a work tool to get you from A to B and forget it till the next service comes up
Imagine it as more of a complete attitude change than just changing from one marque to another when it comes to Alfa ownership and you will be ok
To avoid it happeneing again, take the car out for a 30 mile + jaunt down the motorway once every few weeks at a constant 60mph to give the carbon a chance to burn off gently...
Also bear in mind that a JTD is just like any other diesel especially as its a similar engine in Saab Tdi's and Vauxhall CDTi's, all suffer the same issues!
Yet in Fiat Commercial vehicles the very same engine is used too, yet they don't suffer the same problem...
Easy, they aren't used on a short journey, allowed to go cold and repeat journey home.
Or they are used at a constant long distance & speed all the time and serviced every 8 weeks because of the mileage they do in that period (which includes changing the fuel filter)... And JTD owners still wonder why they have issues????
3. the knocking is either an anti-roll bar drop link or upper wishbone ball joint, the latter being more expensive to rectify... You can check by :
turning the wheel full lock to the right and grabbing the drop link and giving it a firm push and pull, if it moves or clicks, it's goosed and needs changing (in pairs) and not too difficult.
Now turn the wheels straight and grab the top of the tyre with both hands on the inside edge and pull and push firmly and quickly, and clicking and knocking will be apparent and can be confirmed by doing it single handed while the other hand is on the upper wishbone ball joint, you will feel play in it and that also needs changing in pairs too. the oppsite side wont last long if not changed at the same time... More difficult if you aren't mechanically minded though
If there is no play in either item, then it is probably the anti- roll bar bush on that side that is worn... Don't ask!