hesistant car HELP Options

[peroxwhysm00]

a few weeks ago i decided to clean out my car, inside and out, vacuum,wash, wax etc, so then i had more time and i was bored, so me n my buddy went out to autozone and got engine cleaner, went home, and started to spray everything and basically clean everything up, hoping to make it a little more nicer looking...

so of course i took off the air intake, and put a cloth inside the throttle body, so when i LIGHTLY washed down the car with water, nothing would get into it...

from there i was driving my car for a week OR 2, and my car is hesistant at times when i floor it...i would feel that i lost power at about 3500 rpm, and it would slowly go up to 4500, then it feels like i have all my power back at 4500 (feels like a VTEC<< its cool but still besides the point)
and if say i shifted the car to early, it would start knocking and shaking,when before it wouldn't do that, it would just result in me getting to a higher speed during a longer time duration...car never shakes like that (us stick guys know that)

so from there i looked at the basics and started diagnosing...

1. i checked for a misfire ----- NONE

2. i purchased a new cap and rotor, bosch spark plugs, and new spark plug wires----NO LUCK----

3. Then i looked at the battery terminal, and i saw the -negative- terminal was loose and i could pop it off it i tried without loosening it...so i bought 2 new battery terminals, and hooked them up, thinking maybe somehow the voltage was acting strange because it didnt have a good connection...-----NO LUCK----

4. I thought maybe its about time i put some dry gas in my car, to get rid of any water that may have accumulated throught its life...put some in 1/2 tank, ran it till its was empty, then filled up the tank, and added more dry gas in there, ran that tank out, and STILL -----NO LUCK----

---------------------------------POSSIBILITIES IVE ASSESSED-----------------------------------------------------
1. put the stock air intake/box in, and hook up the sensor that i originally took out to get the air box out (i think its a mass airflow sensor, andwhen i got my cheap autozone intake, there was no place to put the mass airflow sensor in, so it was just dangling, and i think that MAY have not calculated the right amount of air needed to go into the intake

2. Or it could be a retarded timing belt, i dont think it is, but it may be....

HELP if you can please, i think the installation of the cheap intake with nowhere to put the mass airflow sensor in messed up everything... from experience, have a guys had any with that or with a cheap intake ??

thanks a lot if you can help