first up, unless you are planning to do some serious drags, can I suggest moving to IRS. Keep the early rear subframe with the horns and convert this to IRS. Gearboxes are your next drama. Either an Lbug box with albins gears and superdiff, a bus box with special albins gears or a porsche G50. More power = more $$$
Then make up a kafer style brace like this one....
http://www.csp-shop.de/cgi-bin/shop2/shop_main.cgi?func=start&wkid=2477153725
avoid the b#gpack style as it puts a bending load along the long bar that should brace the shock towers. Obviously you also need a different engine mount bar too. I'd also look at adding some extra framework to the rear of the car to stiffen it up, because they were never designed to support the power and torque of an EJ20. I'd compare it to putting a 350chev in an FJ holden.
I don't think you can find an OEM cover that will fit. You could graft in a bus engine cover surround and make up a fibreglass cover that bulges up and over the motor. Alternatively, a false floor that is a few inches higher will give you less space in the boot but a neater installation. you could put everything under it. computer, tanks, intercooler etc. I've seen a UK build early square with such a setup and a 993 flat 6 in it. The false floor in his car was perspecs so you see the motor under it. very cool, but not much boot left.
As a man who's kept 5x205 rims on his buggy, I wish I hadn't. There are a heap of others avaible in all sorts of stud patterns, wide 5 is the hardest to get anything in unless it's classic looking or offroad racing rims. there are a number of disc conversion for them, front and rear, but it won't be cheap...but then I guess you already know that, right.
😉
Anyway, I guess the point is, if you want to do it right, it will mean doing it such that it won't be easily reversable. I can't really help you with the efi side of things except to say, there are new rechipping systems for the later ej20ts and they are supposed to both excellent and legal. I'd talk to MRT or quickfit motorsport about them.
There are a heap of guys who've done EJ20ts into notches and fasties and a few into squares. Hopefully they'll still their noses in here as well.