Odd noise

I recently put on the 70mm throttle body and trick flow intake plenum. I already had a BOMZ cold air intake on it. Now it makes a relatively high pitch whistling noise just be for half throttle. Is this normal?

Also, when putting in first gear, the transmission or rear differential makes a loud clunk. Also heard this once when shifting to second gear. Any ideas what this might be?

Last, but not least, going to put on steeda underdrive pulley system and pypes x-pipe w/ cats. Any tips for installation? Especially on the x-pipe. The manufacturer doesn't give all that descriptive instructions.

Thank you!

Check to see that everything is sealed and tightened. As for the x-pipe, make sure you let WD-40 soak on everything and have a breaker (plus a pipe to attach to it for more leverage) since the manifold nuts are a PITA.

everything is sealed. i even went back through to make sure the bolts didnt come loose. I could still hear the noise over the radio. I put high temp gasket sealer around all the edges. Still the noise presisted

I am hearing a thud or clunk noise coming from aronud the rear axle or maybe even the trans. when i put the car in first gear from a dead stop. Also the noise will repeat if i shift to hard into second gear. Any ideas on what it could be???

I changed my plugs recently with the bosh platinum 2 and the idle is rough now like if it is missing every couple of cycles or strokes making a noticable shake of the engine. When i was installing the coil over plugs i was unsure if the coil went properly on the plug. How can i find out if the car has a miss in it and if it is one of the coils because i did not properly seat them???