Another guy on here had the same issue, turned out to be a lead (too much resistance when trying to ignite compression), I recommend to swap 2 leads around and see if the issue stays on number 3 or moves.
What is worse is when you buy some large scale die cast cars from The Warehouse and one day you let your son play with them and they get destroyed, a few months later you look on eBay and they are selling for 4x the price you paid, FML.
The brand 'welly' has a few late model Toyota models:
http://www.wellydiecast.com/product_list.php?brand=Toyota
I have the E140/E150 corolla, number is 44015 but it isn't listed on the website.
EDIT: Not 44018
4AF fly cuts in the pistons should be the same regardless if it is an E or C, compression is the only factor that will change the piston depth but they are most likely the same in that regard.
If the cylinders are not worn then there is no point in going oversize, pull it down, measure it, if it measures up to be within specs then hone it if it doesn't then get it bored.
I know it is a different motor but with the VG you can pre oil the lifters prior to installing but you can also put too much in and it holds the valves open otherwise you put them in and the oil pressure bumps them up to where they need to be.
Shaved the head and put it back on without adjusting anything.
If it is like any over head cam hydraulic lifter then they pump up to a preset volume, correct me if I am wrong but I don't see the lifters in a 5k being that far advanced that they auto correct themselves.
EDIT: where I got the clearances from - http://www.club-k.co.nz/Forums/viewthread.php?tid=6801
Did a search around and this is the best I can find:
Valve Clearance
Hot
IN; 0.20mm, 0.008in.
EX; 0.30mm, 0.012in.
Cold
IN; 0.13mm, 0.005in.
EX; 0.23mm, 0.009in.
Oh, well I would say that there is your problem, when it heats up the gap closes, the valve was most likely pushed open a little bit and it didn't like to run at low rpm.
Adjust them and I bet it will be fine.