Chip replacement is very easy, just make sure you are not changing them with socks on while dragging your feet across a shag carpet and rubbing a balloon on your hair...in other words static is the enemy. Touch a door knob or light outlet cover before you start.
http://web.archive.org/web/20041124234744/www.tech-session.com/kb/index.php?page=index_v2&id=41&c=4
I had issues getting my car to pass inspection also when it was still almost completely stock. Look at my thread here for info on how i eventually got it to pass. Specifically look at the last page around post #40. I think the #1 issue with mine was the CO adjustment screw on the AFM was way out of whack.
http://forums.rennlist.com/rennforums/944-turbo-and-turbo-s-forum/442615-failed-nys-emissions-by-epic-proportions.html
I live in the Metro NY area and we have to deal with the emissions dyno on pre OBDII cars also. 25-years old and cars are exempt.. 3 more years to go on my 951. There is some talk that NYS is going to get rid of the emissions testing and just make it a safety inspection. NYS is broke and they are voting on doing away with the program. A buddy of mine has the emissions equipment at his shop and something on the dyno breaks probably twice a year. Repair is usually a few $k every time a tech has to come down..and they get maybe 5 cars a month that are not OBDII. Flat rate fee is i think $35 or something like that to run a car on the dyno. It takes close to an hour to warm up the dyno and get the car strapped down, run it..etc. Most shops you call now days just say the dyno is broken as its basically a loose loose situation for them. Waste an hour doing an inspection for someone and get $35.. or not waste your time and do ~$75 an hr normal service jobs. True they might find a car needs brakes or other work to pass inspection..but usually its still not worth the time. The amount of pre OBDII cars still on the road is pretty small, i would bet less than 20% in my area.