Front end makes occasional noise when driving down the road. the problem seems to occur most when pressure is placed on the suspension by a bump or bump while braking. It sounds alot like something rubbing against the tire because of the sound and the way it occasionaly sounds like it rotates with the tire

are you talking road noise from the tyres
or exhaust or suspension noises

used tyres matching for noise ...
depends on tread pattern and how much thread
what year they were made

tyre pressure ...sure check all are to spec

pre inspection before any wheel alignment
should will be checking the suspension condition

ck struts and ball joins

Check for leaking rear shocks or a loose sway bar.

What is a Vitz?

Vibration from about 40-60 mph is usually attributed to wheel balancing, but the onset when you hit a bump seems to indicate play in the steering linkages (tie rods etc) or suspension members and stabiliser bar rubbers but you had that all checked out, that brings us back to the wheel balancing.

It's hard to tell, from your description, as to the extent of the clunking.
If it seems to only and constantly occur whenever in forward motion, bumps or not, then I would first check your rear differential, (if 4x4 then your front differential as well).
Check fluid level(s) and if okay, remove cover and check for worn gears and any metal shavings on the magnet on bottom of housing.

Worn gears can toss your vehicle around, any make stomach turning clunks and other awful noises. I've recently replaced a front differential on a 1994 Dakota. It would make same clunks as you describe and a few times would make my back end seem to 'hop' while driving highway speeds. I would check this quickly.

If it only seems to happen over bumps, then your guess on engine mounts or bushings is probably the best guess.

The bushings to the front suspension are completely worn out. They must be replaced before the shock damage your other suspension parts.

Upper strut mounts aren't prone to rattling or knocking as they are usually under load all the time. Very few cars do not have a swivel bearing - a few old Fords are all I can think of. Most current models have the swivel bearing integrated into the strut mount, the main job of which is to insulate road noise from the body. Some cars use a swivel bearing fitted between the strut and lower spring cup.

Worn shock absorber internal valves can be very noisy over small bumps and road undulations and wear in steering rack components can make similar noises especially the rack slipper bearing, the rack end support bearing and the rack end joints.

Many track control arm ball joints have an internal spring to compensate for small amounts of wear. When such a joint has worn significantly it is not always possible to detect free play with hand pressure but they are liable to make noise on the road.

Struts that are housings fitted with shock absorber cartridges retained by a single large nut - the nut can sometimes be loose by a small amount causing the cartridge to knock inside the casing.

The strut piston rod and bush is subject to a great deal of force from the reaction of acceleration and braking and considerable wear can take place between the rod and it's bush. The trouble is any free play cannot be detected when the vehicle is jacked and the wheels clear of the ground and similarly cannot be detected with normal force when the vehicle weight is on the ground. I find lifting the car until the suspension is only compressed an inch or two gives the best chance of detecting wear though considerable strength and energy is still needed.

bad strut mounts are a common problem with the aura

My guess is a strut bushing/bearing, but have your front end checked out by good shop to make sure it isn't something else more dangerous.