Thanks ahead of time!
FYI, this all started when I turned off the engine while waiting for a slow drive thru line. When it came time move, I panicked a little and ended up revving the engine real high during start up.
Since then I noticed that when I accelerate from rest - but after the truck is moving - it feels like not enough fuel, or air, or something is getting through and the engine stutters a few times before taking off smoothly. This also happens if for example I switch to a higher gear a little prematurely. If I down shift causing the engine to rev it stops. Also, if I rev the engine a little in anticipation of the stutter, it usually doesn't happen. I started getting lean fuel codes. I have replaced the air and inline fuel filters, the fuel pump, cleaned the MAF sensor, and someone else replaced the air intake manifold and head gaskets - which apparently were in awful shape. All of these were overdue probably and cleared the codes, but they didn't totally cure the "cough". After a bad episode like in stop go traffic, I'll get an engine light. But usually it will clear on it's own by the next time I drive. Any ideas? This doesn't feel related to clutch / transmission. Someone suggested the oil / air separator, but I'm not even sure my model has that? I plan to replace the PVC valve next, but at this point I'm just guessing. Also, I replaced the spark plugs about year before this issue started when I was getting some firing codes, which fixed that.