Ur car is still new. Actually the OEM Bosch brake pads provides quite ok bite, but only after u've driven the car for at least a week or two. Contrary to what most ppl said, the OEM brake pads needs bedding in as well. Just drive as u usually would, but be careful with the brakes a little bit. After some time it should be fine. The downside to Bosch pads is that they wear out pretty quickly & generates a lot of brake dust around ur front rims. And of course, the cost to replace it with the same Bosch pads can easily buy u another 2-3 sets of RS 550'C high performance brake pads. But other than that, it's fine.
Gear change may be slightly harder than usual due to the fact that ur car is still new. I've got a friend who owns a Saga BLM, same case. While new his gear & clutch feels firm & hard, but after some time it began to loosen up a little. Think of it as ur virgin bride spending her first night with u. Everything is gonna be tight & firm but after some time it'll loosen up.

The wiper sound that u heard is the relay noise. At a higher speed the noise is inaudible, but at Intermittent or Speed 1 the noise is pretty obvious. This is perfectly normal & happens in all PE. It's possible to eliminate the noise totally by replacing the relay, but the solution is pretty costly & it's a no-brainer's way of spending money.
The ignition light going on & off may be a case of loose O2Sensor or loose fuel cap. Actually, the check engine light represents most, if not all of the sensors in the car from O2Sensor to crank sensor, to fuel pump sensor and even brake light switch sensor. Ur car is still new, so I assume it's still on it's 1st tank of petrol. Do the basics first; check that the petrol cap is locked tightly, and then open up ur front hood & wiggle the green cable that connects to the O2sensor to ensure that it's tight and not moving around. Then drive on for another few days. If the check engine light still comes on, drive to the nearest Proton SC to have it checked with PDT. The PDT will display the error code & the source of error that causes the warning light.
As for the knocking noise, the newer batch of PEs now comes with rubber insulation around the steering assembly pipes. But from my personal experience, the noise will come back after a few months even after the rubber insulation is installed. Just pray hard that the noise doesn't come when u're driving over uneven road. If it does, make a complain & have the SC to change the whole assembly for u F.O.C..
The air-cond hissing noise is pretty normal. That's the compressor working its' @ss off to cool the car down. Try fiddling around with the air-cond temperature setting a little bit. The hissing noise that u heard is the air cond gas being pumped in, while the 'kick' noise that u get is the compressor starting up.
For the RPM thing, check if ur idling RPM is below 1k or at exactly 1k with the air cond on. If it's any higher than that, ur RPM timing is out and this may cause ur FC to shoot up. Fret not, the RPM can be easily adjusted via the car's ECU, so u don't have to worry about anything. And as many other members here already mentioned, the CamPro engine is a high-rev engine compared to many other engines in the market right now, and the climb from 2000-4000 RPM is slightly quicker. So the RPM climb shouldn't be something that u should be worried about.
I guess that answered most, or if not all of ur questions. Happy Persona-ing, and welcome to PPLYN!

The compressor kicks in faster or slower depending on the AC temperature setting in the car. If it is switched to higher temperature (warmer), it kicks in less regularly. If it is switched to lower temperature (cooler), it kicks in more frequently and the compressor runs longer than usual.
It is highly recommended that the brake pump to be replaced, ABS & EBD to be added as well if the rear drum brakes were to be replaced to disc brakes. This is to ensure that the braking force is evenly distributed to all 4 wheels and also to prevent the wheels from locking up in an event of E-braking. The stock brake system & brake pads, however, is adequate for normal & everyday drives. If only the brake pump is replaced, the chances of wheels locking will be higher, and this is extremely dangerous especially if u're going downhill as a light tap on ur brake can lock ur wheels and cause skidding.
U're not getting used to the brake. It's the brake burning/bedding in & getting used to ur feet.

Caltex FTW.. Finally another Caltex supporter.. Caltex Havoline is a good engine oil for PEs, but sadly till now only I myself used it. I've never heard of any other members using Havoline Fully Synthetic on their PEs here yet..
U sure the dashboard not so plastic? Last time I took out the stock Wira dashboard trims around the aircond & HU to replace with new one that looks nicer & feels better. The moment I took it out, I 'accidentally' dropped it (on purpose actually, to test it's strength after 14 years). It dropped to the ground & literally shattered to a thousand bits. Just so brittle & fragile. The accessory shop fella told me that this happened because of Malaysian weather and also because the plastic used are of low grade. So make sure u tint ur car & cover it with a dashboard shade if u were to park under the sun for a long time to protect ur dashboard & ur interior trims.
the dashboard was wrap by one layer rubber,tats why i mentioned tat is not so plastic as persona lo..hehe..