if you go with a bigger intake manifold and tb youll want to put cams in it atleast because you dont need the extra air flow on the stock cams you will lose power not gain, happened to me when i put a skunk mani and 68 mm tb on the exact same setup your going to run i-h-e i also had a vafc tuned as well. with the stock mani and tb on my b16 put down 151.3 after tunning. but when i went to the bigger mani and tb with tuning i droped to 146.8 so now thats why i turbo. with the skunk mani and 68mm tb the dyno chart didnt peak wanted to keep climing after red line meaning i needed cams and bump the rev or turbo and thats what i choose. but to answer your acctual question
1. the afc will be fine with your i-h-e i gained 7 whp after tuning one on the same set up.
2. wouldnt advise getting a bigger manifold and tb without any thing but i-h-e you will lose power.