Engine Probs, need help

I have a 99 civic Ex W/ 1.6 Sohc Vtec motor, with 57,000 miles on the car. So far i have replaced or changed, over the last 5 months.
Fuel Filter, Cap, Rotor,Plugs,plug wires, Spark ignitor, O2 sensor ( after cat). all toll between labor and parts and towing have spent close to $1200 or more. the problem I am having is it misses, backfires and doesnt have alot of power. I changed all the main things ( fuel filter, plugs, wires ) 4 months ago and nothing , then check engine light came on , and it really ran bad. so I made a appointment at the honda dealer ( 90 miles away) on the way there it broke down on me had to have it towed. they changed the spark ignitor , it ran fine till about 25 miles from the dealer and they were already closed by then. so I had a friend check it over and he found the cat was plugged. he gutted it out and it ran fine for about 2 months then it started running like crap again. then I changed the O2 sensor had the codes cleared in the computer ( which when we changed it , it tripped the Knock sensor code ) we cleared that and it ran fine for about 30 miles. check engine light came on again and it ran crappy again, my friend cleared the code yesterday , it still ran kinda crappy but the light stayed off then came back .. both times that the check light came on it was fine till I turned the cruise control on. then like 5 seconds later that light came on. we have tried everything we can think of and even the honda dealer wont touch it cuz of my intake and exhaust ( which Ive had for over a yr). they told me to goto whoever put them on which i did myself, they dont like working on cars with mods done.------- as of 11/2/02 I put a high flow cat and 2 1/4 inch pipe on the car, engine light is off but the car is still backfiring and on occasion it it lacks power or surges when I accelerate. usally only in 2nd and 3rd gear. 5th gear it lacks alot of power and when i let out of the gas it backfires not loud but it does.
I have put alot of money into it since may and still cant seem to get it too work right , Ive got someone who specailizes in imports to look at it but he doesnt work with higher performance cars much so he is stumped. last thursday , I took it to a import specialist whom I had do the exhaust , he spent 2 hours doing diagnostic work and found a crack in the distributor cap.. changed the cap and rotor, which cost me 167.00 and I drove it home and Im still having problems with it. it backfires really bad and 5th gear has no power, sometimes 1st and 2nd gear shakes or surges when i take off and it acts like its going to stall.. also I noticed I have a bad build up of carbon on the muffaler, so Im sure its either running rich or lean , not sure which or why. Ive spent $1200 in parts, labor and towing now. if anyone has any ideas on what to check or try please tell me.. also if there is anyone in Pennslyvania here, does anyone know of any good import mechanics that deal with higher performance hondas. cuz I live in rural northcentral pa , and no one here knows anything about them.
have you checked your timing, have you put a timing gear on there? also did this all start when you put the cat back and intake on? Did you just change the 02 censor by the exhaust manifold or did you do them both, (i belive that the second on on obd2 is right around the cat.)
yeah, my friend checked the timing he said that was good. dont have a new timing gear ( that i know of ). nah I have had the intake on for over a yr , and Ive had the same prob since may its just when i fix or change something it works great for a while and then goes back to the Problem I had before. I checked both of the O2 snesors the one on the exhaust manifold which was ok , the 2nd one after the cat ( or on it rather) was burnt and busted up ( when I had the origanol cat gutted) I changed it first with a aftermarket one from autozone for like $75.00 and that didnt work so I bought a OEM O2 from the honda dealer for like $245.00 . the chck engine light is staying off now it didnt before.
check the voltage on your TPS, sometimes if they are off it will cause a "surge" in gear at partial throttle.