Well, since a 5 speed conversion is gonna run you minimum $800, maybe less depending on if you have some parts laying around, you may want to consider where you want your real money to go. You didn't really specify your budget, but me personally, I would do a killer LS/V build. You can easily get a better, reliable LS/V engine built for less than or around the same cost as say, a JDM B18C; which costs around $4k. Once you decide you budget and what kind of build you want to do, whether it's all motor, turbo or swap, I would look at cosmetic details. Wire tuck and engine bay shave, while most of the time purely cosmetic, they both clean up the bay and can make a lot of room in the engine bay. If you really know what you're doing and you can weld, a wire tuck and bay shave wouldn't cost you too much. Chase bays sells already made engine harnesses for tucked bays, but you could do the same with the stock harness. My personal plans for my DA before the wreck were as follows:
Suspension first. Coilovers, subframe brace, lca's uca's sway bars, c-pillar bar, front and rear strut bar, toe and camber kits, etc. and if I could afford them, some custom BBS RS wheels.
Bodywork next. Fix the surface rust that my DA had and push out the one dent the car had.
Engine last. Since my DA was also an auto, convert it to a 5 speed, then do an LS/V build. B16 head, ARP head bolts and studs, CTR pistons with crower rods and arp rod bolts. New spings and retainers. GSR cams with AEM adjustable cam gears etc.
But I'm 17 and live in fantasy land. Once I'm out of college and have a full time job and actually have this kind of money to put in to a car (around $10-15k not including cost of the car) I will. Till then, I'll stick with my bone stock EM2.