The throttle body is the easier of the 2 to clean, in that you remove the plastic piping from the the front of it, and using carb cleaner or throttle body cleaner, you spray it down really good, getting into the air bleed hole and the throttle blade really good.
To clean the EGR port out, you'll need a gasket for the upper plenum, and a EGR gasket. You remove the EGR valve and upper plenum (4 small hoses, and the throttle and cruise control cables, the G101 ground cable, and the nuts/screws for the plenum halves. Now you remove the upper plenum half and with some shop towels plug the intake ports (to keep crap from falling into the engine)and then roto router the EGR port (you'll see the build up on it) from the egr mount thru the manifold opening. It goes from round to square, and most of the carbon builds up on the square portion. You can't clean the port without removing the upper plenum, it's just not possible. BTDT and it didn't work.
Ideally, you would want to do both the TB and EGR port cleaning at the same time while you have the upper plenum off. This way you can get at both sides of the TB, and using the same cleaners, clean the inside of the upper plenum of carbon deposits. You can also clean the IAC valve too while the plenum is off.
Note; done at the Honda dealership, this is a 4-5 hour job plus parts. I've been quoted at my local dealership of 400 just for labor, plus parts for cleaning the EGR port. I got an intake gasket kit thru Rock Auto, and spent the 4 hours of labor doing my wife's 00 Accord. I also replaced the valve, since it had an EGR code present. This was back in 2016 when I did it.
I'll admit I skipped over some of it, but since you've got a FSM, the instructions are right there in it to do the job (what I used when I did my wife's car). I hope this helps.