The One'$

ok i recently bought a 96 honda civic ex. when i bought it , it already had a differnet motor in it (d15z1 vtec w/ 98 head) i had it for a while and out of no where my engine got messed up, the crankshaft was broken. so then instead of buyin another crankshaft i decided to buy the whole engine again, so i went to a local motor store and bought the same motor this time i bought it with everything original (d15z1 vtec) now my car is running good except what i realy want to know is why it wont let me go past 5500 rpm. everytime i try to go on high rpm's it sounds like 2 metal peices rubbing up against each other. i personally think that its the ecu because the ecu is not for that motor, but i really dont know waht it could be. any suggestions????