Bad lifters can make a heck of a racket.
Physically, they are located just above the crankshaft in the block, well south of the head and could easily be confused with a bottom end noise.
I would hesitate recreating the condition anymore than absolutely necessary, anything that causes bad noises will surely cause damage.

An engine needs to breath, if it can't bad things will happen.
I have seen bad Cats cause gaskets to blow out, EGR components to melt and sometimes all sorts of weird noises.
Just try going for a jog and breathing in but not out and see how long YOU last.

Checking the cat is so easy to do, it just makes sense to rule out that possibility.
They have flanges and 2 bolts (and a gasket) on either end.
You only need to split the connection at the forward side (closest to the engine) and look inside.
You'll see a nicely formed honeycomb inside, if you see blobs or gobs on the inlet side (or if it's broken or cracked), it's toast.
I would have new gaskets on hand (fresh bolts would be a good idea too), best not to try to reuse those bits as leaks are sure to follow.
This would be a $20 and 3 beer type of "investment" and maybe an hour of your time, well worth checking if just for peace of mind.

There is no way of cleaning a contaminated Cat, replacement is the only course of action but it is still an easy thing to do, especially if you replace with either OEM (big bucks) or A/M, if you go A/M make sure you get a "direct fit" as it will be a simple bolt in with no mucking about required.
Further, Cats don't "fail" they always get taken out by something else (either from running rich, lean or excessive oil consumption) if the cat is bad you WILL want to make sure you fix whatever caused it to fail.

If the Cat is good on inspection, then move onto the fuel filter. As you don't know the history, it's worth changing it out.
Fuel filters are relatively cheap too, just make sure you get new gaskets for the banjo fittings (if going OEM, they don't come with the filter)

But you'll want to do things in a logical manner. (easiest and cheapest first, then work your way up)
The more variables you eliminate the easier it will be to solve the issue.

I am NOT saying there are no issues internal to the motor, but it doesn't sound like they put much effort into the diagnosis.
BB