nope the car is running smooth i have had it for approx 4 years now. There were gear related problems in first year...that is not mechanical failure...and it can not be considered a problem...if you try to run normal gears with such engines. i tested and when i was sure that won't work. i changed the complete transmission setup. r154 (supra's 5 speed gear) which is built for this engine. and since i knew i was going to run high boost. so instead of normal clutch kit i imported ACT stage 4 clutch kit which can hold upto 500rwhp. Most ppl install the clutch kits and don't finish the initial running which requires you to drive 300-400km without boost in normal traffic so the clutch can break in and adjust. i completed the running which was a pain (driving without boost lol) but after that i haven't ran into any problems. So if you spend money and provide the car things it needs to run properly. i don't see why it will give you problems.
p.s engine itself never gave me any problems in 4 years. which is quite impressive as before rx8 i had civic 95 and even in stock cars with factory fitted engine you have to visit workshops once/twice a year. But 1jz vvti is very strong engine and even if you try you will need skills to break it or cause problems lol.
i hope this answers your questions. you can't expect to spend money on just engine throw it in car and then expect that it will run smooth forever untill or unless you provide it the required setup and conditions