Hmm, if you swapped out the harness from a manual also, then everything should plug up and play I would think. That clicking could be your ignition switch going bad. Mine started messing up on my old 240 and I would have to wiggle the key while trying to crank it, it would click and eventually it would start up. Now I've a different chassis altogether but the only thing different with the ign. system is the ign. switch and it cranks fine..but if it crunk up fine before then it shouldn't be the switch. It could be something else with car, get a buddy to turn the key while you hunt down the clicking noise, could be a bad relay somewhere.
Starting mods are pretty much just:intake systemheader, test pipe, cat-backunderdrive crank pulley redo some engine ground wiring with better wireelectric fans
of course you'll want to replace the distributor cap and rotor, plugs (Autolite Platinums from Wally World did fine for me), plug wires, fuel filter, tune-up stuff before you start getting into upgrades, a car in need of a tune-up responds poorly to mods.
I saved a few nickels by (at first) just removing my stock airbox and throwing a cone filter on, grabbing some extra amp wire I had to improve some grounds under the hood, and getting a pair of electric fans off 93-97 nissan altima (i think) for around 20 bucks at a U-pull it auto salvage yard.
Ebay and some other sites have cat-backs for around 150 starting out, I've heard 'this and that' with headers off of ebay, mostly fitment issues so search first and read up on people's experiences with different brands. I myself never got a header, never got a cat-back because every nut and stud on the exhaust system was rusted to hell and back, I figured I'd just leave it. I'm thinking about getting an ASP lightweight crank pulley next.
Engine-wise, you've got the ka24DE which uses the same block as the ka24e but has a different head of course, needless to say it drops right on in. The sr20det (s13,redtop,blacktop) drops right in also, but there's a little bit of wiring you'll have to do since it uses a new harness and ecu. I don't know of what other motor can just drop right in without modification to the motor mounts and driveshaft and such.. used ka24de's are pretty cheap but I mean really you don't know anything about the motor until you do a compression test. You could snatch a twin-cam up and leave it in the garage or wherever and build it up over time and prepare it for a turbo
http://www.youtube.com/watch?v=E2jSnrcz5c4