sounds to me like you have left the vacuum modulator hose disconnected?
If so third gear wont engage until you reach 85 kmph
Amazing that only 4 little bolts hold the torque converter to the flex plate eh!

woohoo good ol narrogin rev heads action at its best, there all here coz there not all there!

I would say try bringing your timing back to 5 degrees and either reduce the size of the air correctors on top of the emulsion tubes down a size or increse the main jets up a size until you are happy with the results.
Once you are happy you can try the full throttle plug test where you hammer it until red line on a issolated piece of road in 2nd gear then immediateley put the car in neautral and switch the engine off, brake to a stop and check the plug colour for lean or rich main fueling conditions

what is your spark plug gap like?, points gap? valve clearances and compression tests looking like?

yeah mate I think I was having problems with the spark plug gap being set at .044"
I put new plugs in that were set at .033" and some injsctor cleaner in the tank and i replaced the fuel filter and it has been as good as gold since. I think I will try some irridium plugs gapped at .044" to see how they stand up and i will test out a pair of 155 main jets too just incase it is leaning out at about 7000-8000rpm
edit when I took the old fuel filter off of the fuel line from the tank, some bubbles esacaped for a few seconds before fuel began trickling out so I might have had a problem with air capitating in the pump causing the problem by running out of fuel intermittently in the fuel bowl

I have a Hi-Tech header, into a 2 1/2 inch pipe all the way to a lukey offset 2 1/2 inch muffler and straight over the diff and out the back, it sounds LOUD, a little TOO LOUD. I am looking into fitting a resonator right now! But it sounds awesome at full throttle at about 5000-68000rpm

also when I replaced my A12 with an A15 I tried to bolt the auto box onto the engine and realised that I couldn't get the transmission case perfectly lined up with the back of the block. I got underneath the car and busted my guts rocking the motor back and forth and shaking the transmission from side to side, after about half an hour I looked at the torque converter and realised that the torque converter lugs actually sit inside the flex plate, the bolts only hold those lugs in the flex plate and guess why my transmission wasn't lining up? yep those lugs were not sitting in the flex plate duuuh theres another blonde moment for me

have you tried the wreckers? ask for 120Y struts complete with discs, hubs, calipers and if you haven't already got one, get the front sway bar and sway bar mounts too, then when you put it all together use your current strut tops with the 120Y struts to maintain your current height and remove the check valve from the front master cylinder circuit to prevent brake drag on the front calipers.

how much money do you have!? about $700 au will get you a decent 63a box they are bloody tough units and bolt straight up, or like pepper said get a calica 5 speed and buy a dellow conversion kit and you should never have problems again.
Gear boxes are precision units if you buy one cheap have it checked over for any underlying faults, a worn bearing or synchro ring will spell torment for you if left unfixed. Best bet is to do the job once and do it right that way all thats left to do is enjoy driving it with no worries at all

yep righto I shall try some injector cleaner in the tank, I have a 770 cold crank amp and 105 amp hour dual cycle battery in the boot and it is chargine well off of the stock alternator, I charged it right up before I installed the set up and it has a small visual indicator that lets me know if it is fully charged, low charged or completely flat.
I had an idea today that I should drive the car till it is warm then take it to a quiet piece of straight road and accelerate to the point where the engine starts missing then quickly turn the engine off and put the car in neautral and come to a stop. Then I will check the fuel level in the bowl, if it is empty then it is running out of fuel and i will need either a new pump or the filter could be blocked ( unusual since it is only a few weeks old)