2000 Honda Civic engine starting problems

Engine Mechanical problem
2000 Honda Civic 4 cyl Automatic 65000 miles

we swapped the engine from a 2000 honda civic ex automatic into a 2000 honda civic si manual transmission body. We put the ex engine and transmission along with the main engine wiring harness and computer into the si. We got it to crank but it won't crank all the time. When the key is turned to the second position it makes a continuos clicking sound and when I try to crank the car it turns over but wont start. I did get it to crank a couple of times and I think that was when the clicking noise stopped after a few seconds then I turned the key fully and it started up. Could the clicking sound be the fuel pump.