As most of my design use more than 16K now, i always use the Bootloader. Never had manyt problems with. The only problem that persist, and it's not a big one, is when i use the compile/program Button. Sometimes it works sometimes no. I have a message like "Reset target processor' blah blah. No big deal, use compile, wait 1-2 secondes, then program the PIC... must be caused by a slow machine.. i don't care too much about that problem..

I'm not a big ICD fan/user so i can't really comment one. The only thing i could suggest is, as you said, use multiple Disable/Enable... Sorry, this is not helpfull

Sure you must run your PIC at least @20MHZ for better results