There is one hose behind the thermostat which fails so make sure you replace that one. Its a painful exercise to replace but it does need to be done. It takes all day to remove the turbo and surrounding parts to get to it! 
Also make sure you pull all the cover panels off the inside of the car to check all the wiring to make sure its all in good order.
Did you have the CV joints checked when you had the clutch replaced?
Did you change the gearbox oil?
At the end of the day there are many things you can check. These are the few I have had trouble with in my Hardtop 3SGTE.
 

Falcon
Check the threads in the bellhousing for the front engine mount.
They can get ripped out with abuse or neglect. That may be the reason it is missing.
Helicoil can repair if needs be.

The threads on the firewall were fine but i couldn't actually see where the bracket bolted to the transmission.
There have been lots of missing parts so I'm hoping it was just donated to another car and not stripped out.
 

B24
There is one hose behind the thermostat which fails so make sure you replace that one. Its a painful exercise to replace but it does need to be done. It takes all day to remove the turbo and surrounding parts to get to it! 
Also make sure you pull all the cover panels off the inside of the car to check all the wiring to make sure its all in good order.
Did you have the CV joints checked when you had the clutch replaced?
Did you change the gearbox oil?
At the end of the day there are many things you can check. These are the few I have had trouble with in my Hardtop 3SGTE.
 

I'll try to do as many hoses as i can at once so I dont need to do multiple bleeds. I'm not sure if the CV joints were checked but he did have a good look over it. The axle was loose and grinding so it was greased and tightened. It did get new gearbox oil as well.
 
 

This was my weekend:
 
 
 

 

 

 

 

 

 
Replaced my ratty shift boot with a leather piece from ebay. Instant improvement to the interior. 
The gear knob I bought was advertised as M12x1.25 but the thread is far too small to fit  so I'll have to find something else.
 
I wet sanded and sprayed both side mirrors. The paint is a very good match. Not perfect but much better than before. I didn't use any clear-coat as I didn't think it would work with the original single stage paint. In hindsight it could have done with a light coat of clear as the body still has some shine left in it. I'll add some clear when I get a chance.  Itching for it to be properly driveable.
 

I did some more painting / tidying yesterday, this time in the engine bay.
Heat shields and piping removed

 
Cleaned up most of the surface rust and painted

 
Starting to look better

 
This is how it looked when I got it

 
I've got a red valve cover that I'm tempted to install, but don't want to create new problems with the gasket and studs. Bigger fish to fry at this stage. I'm waiting on four parts orders at the moment, the delivery time is killing me.
 
Once the brakes are sorted (plus clutch master/slave and ball joints) I think I'll ramp up my search for wheels and tyres. I've been tempted by a few used 17x8/9 sets but worried about inside clearance when I ultimately get coilovers. It looks like 17x7/8 is a safer bet but finding anything that a) fits correctly, b) looks reasonable, c) doesn't cost a fortune is no easy task. I'm tempted by PrimeMR2's RPF1 17x7/8 set but $1,000USD for shipping  not happening.

Engine bay is looking good.
 
I did my heat shields recently too. The big one was beaten to hell over the years to make it fit haha.

Lol i can imagine. Mine came out alright but took some bending and smacking to get back in

You did it with the turbo still in yeah?

Deevon
You did it with the turbo still in yeah?

Yep turbo still in place. All I removed were the parts shown in my paint booth (balcony table). 

That would have been fun, was annoying enough without the turbo 

I finally installed my front brakes this weekend. New disks, EBD red pads, rebuilt calipers, and some paint.
I followed the bed-in instructions and all was well, until the car died on me... One step forward, two backwards with this thing...

 

 
Big improvement in performance and appearance compared to the rusty pic a few posts back. 
 
I also installed a front engine mount and some missing trim pieces in the front bumper.
I'm part way through painting my new (used) wheels and will post up when finished. Hopefully I can sort out the stalling issue in the meantime.