@jz,
Thanks for the details. 
Below is my opinion about all the work done.
Catalytic Converter and piping. I think by removing cat converter, there will be some gain as you mentioned. But we should see that by removing cat converter, will there be any negative effect on the engine? If there is no negative affect then it can be done. for the middle sound box, I think you can keep it and you can change the piping beyond the middle sound box to 2.25". In this case sound will be less but power can be increased.
Catalytic converter needs to be cleaned after specific period of time. did toyota mechanic recommended you to clean the CAT converter?
About all other stuff, I think this was the right time to do it but keeping the expenses in mind, I think they can be divided into two steps i.e. you can do some part at 30k or 35k and the remaining at 40k.
I have few questions for you.
1) According to you, what should be the right time to replace brake pads?
2) When should be the Brake fluid changed (both in terms of millage or time).
3) From where you purchased the oil filter? because last time I purchased oil filter from toyota walton and its cost was more than 1100/-.
Thanks,
