I think you have the right idea. Wheels and tyres will make a big difference so definately do those first. I would get some miles on the car before you tune, having said that you could have issues at any point. My gearbox started having issues as soon as I had the tcu mapped.
A mate had custom code stage 2, downpipe, intercooler, forge elbow and intake pipe done this weekend gone. Did 540bhp / 550 ft lbs. Aparently highest figures they have seen on a stage 2 and confirmed the elbow definately makes a difference.
Everyone should just replace the Pzeros with PS4S', after 8k on the pzeros mind were on the wear bars and had 0 grip at all. They also made the car creak when moving slowlt with full lock. Have PS4S on now and it's like a totally different car.
The beeping noise is just a vibration coming from the valves. I had the same thing in my focus RS which uses the exact same valves. Sounds like an electronic beep from inside the car but it is infact a vibration through part of the valve mechanism. In the end just unplugged the valves and used a...
Definately not normal, at least on the facelift. No one that I have spoke to who owns a facelift has said they experience the same thud as mine. And my tuner says this is the first they have come across (fl) that's doing this.
Is it like a loud thud when it changes to 2nd gear? I have this and still trying to figure out what is causing it. There is a chance it could be the haldex rather than the gearbox if wheel speeds aren't as they should.