I have an 04 5-speed with 190k and its strange sometimes too under heavy load. it's noticeable in 3rd around 5000-5300rpm its almost like a "vtec" engagement but it doesn't act like vtec

lol, its just weird, doesn't do it all the time but hesitates sorta..
I too have the low idle thing sometimes, but the computer figures it out really quick and it'll find the right idle speed. It's really only after I mash on it a bunch and come to a stop. with the a/c on it'll idle lower more often..
Only thing that bugs me now is the throw out bearing squeels like a piggy when its rainy and cold out. stock clutch, getting ready to order the ACT street