level adjustments don't seem to help

any suggestions ?

turn down your sample down.
drink some OE

Click happens from the wave being stopped when it's not at zero crossing. This is normal. Since the sine wave is really smooth, it's very noticeable.

yea what hseiken said. not alot u can do about it. before resampling stuff together, record a hit of the sub signal on its own, then play with start/end point to minimise clicking. unfortunately u dont have enough accuracy to get exactly on the crossing, but u can get closer.