Have recently been through this exact same process - as far as the flat spot goes; agree with gdt2000 - issue was sorted the moment new rear plugs went in. I bought a new EGR because of all the chatter on this forum; but haven't needed to fit it.
NVH - 2-stage cure (NB - am on 14" wheels - makes things easier):
First stage is to fit good quality Euro tyres, of a model that explicitly prioritises quietness. I chose Pirelli Cinturato 1 Eco Verde - absolutely transformed the noise/harshness issue in a 2002 1.4 SE. Obviously wet grip is first rate as well. Most of the noise seems to come through the front struts.
Second stage for me was to replace rear shockers with KYB Excel-G, & the springs with KYB - these combined transformed the choppy ride of my 85K miler to a nicely damped ride as good as or rather better than a chum's low-mileage 2007 model. KYB are a huge Japanese manufacturer of OEM suspension parts and specifically tune these replacements to the dynamics of an old vehicle.
So I know that this has been discussed to death in these forums but I have read most of the threads and my situation sort of sounds similar but isn't.
a. Flat Spot:
I have noticed that in 1st gear half throttle acceleration, just as I reach around 2500 there is a very noticeable gap in acceleration for a second and then it resumes with a lesser rate.
b. Bucking at Low speeds:
Also since last week the car seems to have started 'bucking' as many threads put it and finally I know what they meant. Happens mostly on part throttle, half clutch situations when crawling in London traffic. EGR I have cleaned a few times, checked front and back plugs (2 of them at random) and they look fine so just wondering what could it be.
The air filter is about 5000 miles old so don't suspect thats the cause.
c. Noise Vibration Harshness
Although there are no knocks or bangs in the suspension, on bad surfaces the car seems to let a lot of vibration in. I have driven a lower mileage Jazz of same age and it felt much more compliant and softer than my one on same 15" alloys so I was wondering if I can do anything to improve the NVH?