A P0300 is a random misfire code not specific to any cyl. If it was a P0306 then you would for sure have a misfire on just the #6, not to discredit your findings just throwing that out there because your problem may not be with just your #6 cyl.
When you pulled your #6 out, was the plug wet or bone dry? I would assume if the plug was wet you would have no spark (which you said you do) if it was bone dry then you have no fuel (since you are sparking, but not firing) You swapped injectors with the same symptoms, did you check your injector wiring? The plug that actually plugs into the injector itself? I have had this issue with a sensor being a short in the plug itself. Look at your plug, look inside it. Is it possible to unplug the plug from the injector and test for voltage/pulse while the car is running? Might be an option...
Maybe a stupid question, but what PCM are you using? Your original or the one from the car you got the L32 from?
As for gas, pppffftttt.. My car sat for 5-6 months with 1/4 tank of 87 while I was building my motor. I dropped in my motor and test drove the car around with that tank. Mine being a top swapped motor and 87 with no KR, I wouldn't think it's fuel related... lol
I would not pull your motor back apart on a whim. I know it's frustrating, I'm dealing with a P0171 code so yeah I can relate to the whole pulling your hair out and blowing the car up..
As for a clogged up intake runner??? I'm trying to think of symptoms... I'm also trying to think if a clog would hold up being wet with fuel, and being pushed on by boost... I dunno, just thinking out loud... Did you hear the motor run before you purchased it?
