Re the smell: Two possibilities come to mind, as they both happened to me - and my 2003 Baja - at different times:
Some time ago, I went to (trusted) shop with a smell of fuel that showed up on very short trips - e.g. from the driveway to park on the side of the road. Turns out that the Baja, as well as other Subies have some fuel lines (or possibly connections - I don’t recall) that lose flexibility and start to leak after a while. This happened to mine I think somewhere between 90k and 105k miles.
More recently, the garage fixed a new smell. I thought it was fuel again (and they replaced those same fuel lines again, at no charge) and they also found coolant was leaking from the engine block onto the exhaust, so the fumes were coming in through the fresh air vent. So they fixed that leak, and replaced a couple of exhaust gaskets (and stopped my heat shield from rattling, and, and…) so now the smell is gone…
Now if only my mpg was back to where it used to be…
Re: the shudder in shifting (mine’s a 5-speed also). Have you tried shifting at different RPMs? I typically shift early and often. Getting started in first, I often let the RPMs drop to 750 or less as the clutch disengages. When it doesn’t stall (less often than it used to be) if I gave it too much gas, there’d be a lurching effect. If I consciously disengage the clutch at 1500-1800 RPM, I don’t get that effect. I just have a mental stumbling block of thinking this is wearing the clutch out too much.
My father used to keep engines between 2-3000 RPM. I’m bent on being more efficient, so I accelerate much more gently and keep my engine about 2000 most all the time.
re: the ‘bumping’ noise… when you next go to the garage, it might be helpful to them if you can tell them that the bumping is, for example, worse turning right, and not there when you turn left - or something like that. See if it changes depending on speed, turning radius, or some other driving condition. Also whether it’s a dull ‘whump, whump, whump’ or a sharp ‘bang bang’. Is the sound related to wheel rotation or engine speed? (Go around a curve stepping on the clutch pedal to find out.) Driving with the windows open near tall walls/buildings/barriers can help you determine which side it’s on. I’ve heard (many years ago) that many Toyotas will acquire a banging noise on sharp turns, which turns out to be a fairly harmless annoyance, but I have no idea if it’s similar to yours.