if you do a full swap(axels, linkage, mounts and what not) then the brake issue wont be a problem. Mike is right, most JDM motors are beat to shit by the time we get them. 9 times out of 10 the rings are burnt, the oil pump is bad and ive seen more than one bent valve in my time. Many places that sell them offer a DOA/parts warrentee that is usually pretty good. Just remember, "buyer beware".
Like many people have done, i stuck with a d16. I built it so i know what went into it but for may people, they spend the time and money on a swap only to find out 10,000 miles later that the motor was crap.
If you want my advise, buy a good motor(b16, b18) and build the internals before the actual swap. That way you not only get the max power right away but you know that you wont have a bad rod or a bent valve blow up your motor.
Good luck.