I think most of your shuddering and misfires are due to , Factory plugs set at varying gaps, this was a well known problem on GEN1 EB . Factory plugs were all over the place. poor quality control. Other is 87 octane in a boosted engine timing is getting pulled these engines have very sensitive knocksensors . You should use highest octane available. GEN 1 EB was a 20 hp diffrence between 87 and 91 octane. Ford rated the HP at 365hp on Gen1 and 87 octane. 20hp increase was due to increased timing before it knocked. I have a fully modded EB 2014 Tremor. On my SCT running a tune and 91 i average in hotter months seeing knock values pull 1 degree of timing or 2 deg. When i know i will be going to the track or local grudge race, I will run e30 and 2 min after leaving the gas station i see the knock values decrease and its adding 7 degrees of timing. When i get home I change over to my E30 tune. Set for more fuel and timing. Weep hole i would not do it unless you see build up in intercooler moisture and oil mix. My intercooler has been spotless inside with 17,000 miles now. I live in a dry climate. For those in high humidity locations the weep hole does eliminate moisture build up because it is drilled at the lowest point where it collects and the hole is very tiny 1/16 of an inch. There is a minimum amount of a boost leak but not enough to cause any issues. What happened to GEN1 motors that blew due to condensation. If you drive normal and putz around a lot in high humidy ,condensation will build up in the intercooler. Then at some point you go to full boost getting on interstate or traffic condition , towing. that slug of water that has collected gets sucked up charge pipe into the intake manifold and you will get a severe misfire and if enough water gets in it will break connecting rods. Liquid does not compress. I only get 10,000 miles on a set of plugs , i set the gap to 28 thousands within 10,000 miles they opened up to 33 and 34 thousands and i was getting a WOT misfire. My Tremor dynos at 425 HP and 550TQ at the wheels.