sorry you're having all those problems. i'm not sure what "bogging noise" is but does this happen both in vacuum and at boost? you mentioned that the car was better with the other intercooler- do you have a leaky intercooler hose? this will cause erratic idle at random, i had the same symptoms from a intercooler hose that split open but was not visible until removed. i take a 3" abs pipe plug (slip on, not threaded) from home depot, drill and tap an air fitting into it, install into flexible hose after vam and pressurize to 20 pounds- if you have a leak it will show very quickly

. fuel pump is always possible but make sure you have fresh plugs and wires- i have to replace mine monthly or the power cuts out under boost. does your car use an iac motor? if that is unplugged or deleted that is your weak idle. remember that your car is after 8/1989 so the iac diode is internal (look for a "D" stamped on the iac plastic body) but the 1986 had the diode externally mounted in the harness. that means that if you used the 1992 harness with the 1986 solenoid you will be missing the diode and have an idle of around 4000 when hooked up. sorry for the long response but just something i wanted to pass on that is not widely known with 2.3t swaps. just in case it is a pump issue keep your boost all the way down until you figure it out- good luck and keep up the questions
