98 civic ex 1.6 5 speed

I’ve got a 1998 civic ex with a problem I thought to be fixed a few weeks ago but that doesn’t seem to be the case. The car bucks while accelerating. It doesn’t typically do it in first however 2-5 it is fairly noticable. Originally it was once and a while then it continued to get worse. Here is a list of recent repairs some due to routine maitnence others looked a little rough or were broken.

Rebuilt 13k ago.
Oil change
New dizzy cap rotor coil plugs and wires
New MAP sensor
Throttle cleaned out
New intake ghasket
New 02 sensor
New cat
New water mount
Timing job

I might be leaving a few out but I believe that’s it. My question is can an axle cause bucking on acceleration? I was looking under the vehicle today and the passenger boot is busted all up and on decel it makes a click (usually one click) when I come to a complete stop. I had no engine light however just to humor myself I hooked my scanner up and I received a p0171 cell under current codes. I don’t have any vacuum leakes unless they’ve evaded me. I just did a seafoam cleaning about 8 hours ago. All my injectors are clicking (doesn’t nessicarily mean they aren’t clogged) and my filter was just changed. Any ideas?