Ticks can be all sorts of things, same bad, some quite irrelevant. My advice would be to go over all those repairs and make sure they are done to your satisfaction. The tyre will probably get plugged (I'm assuming the screw was in the tread not the sidewall) to keep costs down as AWD cars need even tyre wear. The parking light fault will be a $20 switch, or the wire fallen off, and the door luck will probably just get sprayed full of WD40. At a guess (from several thousand km's away) he'll get those repairs done for under $500, so screw him on the price anyway, don't cop any gentlemen bullshit about doing you favours. I'm more inclined to think the clock is not worth fixing because it will dent his profit margin.
The CV joint leak is definitely worth checking, it might be a split boot or just a loose clamp. If its been leaking for a while it might need regreasing, not just sealing up. If the boot is split then the others are probably not far off splitting and are worth doing at the same time. If the clamp is loose, give it a good check for indications of shoddy workmanship. It might be nothing, but its cheapier to walk away now than buy a money pit. I suppose that all depends on whether you've signed anything, just don't be bullied into handing over the cheque until your happy.
On the gearbox meshing, I've had experience with synchros failing before the bearings, we ended up pinning it to an oil issue that can be climate related. You can get oils that are the same viscosity at temperature but are a little thinner when cold, which stops the bronze synchro cones getting pounded. There are a number of affordable quality gear oils on the market that have solved the problem for me bofore, personally I swear by Penrite.
Mr Sheen, what's the recommended oil for the manual transmission, or is it just a bad design like 2nd gear in the T56? I'm not trying to second guess you, just professional curiosity.