I've just bought an SW20 with the NA engine and I have a few noob questions.  My car needs a new clutch, is it hard to do?  It has an unknown timing belt, if I'm doing the clutch should I do the timing belt at the same time?  Is there anything else I should do at the same time as the clutch?
 
My car doesn't have a spare wheel, will a full size wheel fit or does it need to be a space saver?  Will a space saver from another car fit?
 
Where do I put the targa roof panels when I remove them?  Do they fit in the boot?
 

Congrates on the purchase and best of luck with ownership.
 
If you are changing the clutch it will require engine removal so best to do as much as possible while the engine and gearbox is out of the car. 
Oil pump, gaskets, crank seal, bearings, belts, 'hose from hell' located under the exhaust manifold are the first that come to mind. Pretty sure a few others can add to the list.

Welcome to the group.
Targa tops go into dedicated stowage bags and are then secured by straps behind seats.
Full size original spare will fit but it depends on tyre size. Early model cars had space saver spares.
What year model ? Australian delivered or import vehicle ? What are the symptoms of the clutch problem ?
Sometimes it just needs adjusting. If it does need a new clutch make sure to use a genuine Toyota release bearing.
Depending on the age of the car etc a new gearbox input shaft oil seal is pretty easy to install in the S54 gearbox.
Axle oil seals too. Clutch slave cylinder renewed or re kitted as they are a bitch to get to later.
Water pump, genuine Toyota thermostat while it's out.
Do NOT use GL5. gearbox oil when refilling. GL4. only.

B24
If you are changing the clutch it will require engine removal so best to do as much as possible while the engine and gearbox is out of the car. 

 
Do I need to completely remove the engine from the car or just lift it off the engine mounts?  I found a reference to a clutch change guide here on the forum but the link didn't work.
 

B24
Oil pump, gaskets, crank seal, bearings, belts, 'hose from hell' located under the exhaust manifold are the first that come to mind. Pretty sure a few others can add to the list.

  Does the NA model have the 'hose from hell' or only the turbo?  By bearings, I presume you mean the pulley bearings from the timing belt?

Falcon
Targa tops go into dedicated stowage bags and are then secured by straps behind seats.

 
Mine doesn't seem to have the bags, do these come up for sale very often?  Are they expensive?
 

Falcon
What year model ? Australian delivered or import vehicle?

 
It's an Oz delivered N/A car
 

Falcon
What are the symptoms of the clutch problem ?

 
Clutch slips in higher gears, especially if you are rough with it.  I thought that it would have a hydraulic clutch so wouldn't need adjustment?
 
I will make sure I use the genuine bearing, I usually do the axle seals but not usually the gearbox input shaft seals, do these leak often?  I thought about doing the rear main seal but to be honest most the time I mess with them the new seal seem to leak anyway.
 
The thermostat looks hard to get to so I'll change that, along with the cooling system hoses.  I was looking online for a full cooling hose kit but they are only available for the 3S GTE and not 3S GUE.  Are the cooling hoses different?  I figured they would probably be the same but the turbo would have a few extra hoses.
 
What is GL4/GL5 gearbox oil?  I usually just use whatever is factory specified.  I presume it doesn't have an LSD so won't need LSD oil.
 

JME

Falcon
Targa tops go into dedicated stowage bags and are then secured by straps behind seats.

 
Mine doesn't seem to have the bags, do these come up for sale very often?  Are they expensive?
 

 
You don't have to have them. I've never used them.

What year SW20?
If doing the timing belt before buying parts, get the right part numbers (see below) because some 3SGE NA motors are different, and have a different tensioner setup and timing belt.
Also important to fit new tensioner rollers, new water pump front half, but only use genuine Toyota.
A good idea to fit new camshaft seals also.
 
Links for finding Toyota part numbers:
SW20-AJMQF / toyota | fig list｜JP-CarParts.com
Another one but without diagrams:
https://www.toyodiy.com/parts/q_G_1990_TOYOTA_MR2_SW20.html
 
When you have the right part number, a good place to buy genuine Toyota parts.
https://www.amayama.com/en/genuine-catalogs/toyota
 
BTW, as mentioned, only use a GL4 rated oil in your S54 transmission, 
but you will probably have to look online for it.
Don't use anything with GL5 or dual rated GL4/GL5 on the container, because it can mess with your syncros.