You can't really check for engine setups since it involves opening the block, but based on the previous results, you should have kept records of weight, vs. time. There should be a line where the best times will start to look dubious.
Anyway, I wouldn't bother too much on big bore high strokers, those engines cannot last anyway, and lose compression pretty quickly (note: high maintainance)
For the prizes, I don't see much sense in building that kind of engine where the maintainance cost far outweighs the cost of the prizes. For bragging rights, it's a good idea though.
For starters, just make it fun, or start bracket racing where skills are take the mainstage rather than outright power.
Write the time the times the owners expect the car to hit, and whoever hits the closest time to his estimation wins that round. It'll probably be fun even for stock rides.

put 16 secs, then run a 14flat, while the next car puts 16, but nets 16.5, naturally the 16.5 takes the win for that round, because the owner didn't cheat on the est. time. In that case, if the owner knows the car can do 15 flat, he marks the car as a 15 flat, and he has to make sure his R/T's and 60 foot times are constant enough to ensure he hits that 15 mark the closest.
It's also easier for you to categorize the vehicles so that cars with the same time bracket run together, giving the impression of a close(r) race.
Tire wise, I think banning the semis are not a good idea, as another way around restricted tire compounds is using wider tires, 225/40R16 (as an example) anyone? Since it's straight, I don't think having the tires touch the inside fenders is a big deal for them.
There's also cheater slicks with small sizes that look very close to normal tires, but with soft compound (forgot the brand) that people have yet to use, so that's probably something to consider down the road.
I do note a problem with bracket racing though, in that the owners must run their cars before, like in the states where drag tracks are available for the owner to get timeslips and note how fast their car can actually go, while at sepang, it's not readily available.
Of course, for the regulars, I think it's pretty easy for them to guess what times they can hit, since they are regulars after all.