loose nut behind the wheel

i just currently had my heads redone due to broken spring and valve seal leaks. i have had help reinstalling my motor with my uncle everything went back together great. but now when i am driving and give it the gas you can feel and hear some kind of resistance im not sure if it is detination or ignition but my once powerful car is now lacking due to this problem.
i am hoping that its not timing the way to time the car to my understanding is the timing mark on the crank gear and the timing mark on the cam gear you put the motor at tdc on cylinder one then the chain has 2 dark links in it u put one on the timing mark of the cam gear and the other goes to the timing mark on the crank gear and do the same to the other bank.
i also have a clanking noise when the car is in nuetral the pilot bearing,throwout bearing,clutch disc,clutch fork, and folkrum pin have been replaced i had to take the trans. out after reinstalling the motor due to this problem and the inputshaft bearing is in great condition the noise sounds like its coming from the bellhousing ive disconnected the clutch cable and held the clutch fork in my hand and it still continues my under standing is that 5th and reverse are spinning when the car is in nuetral could that be my noise ? it also goes away when i push on the clutch or gently push the shifter torwards a gear while in nuetral