Hello and welcome Justin!
First off, that's an impressive list of projects! Previous knowledge will always help you on almost any car, so you're ahead of where I was when I joined here.
Moisture in your tail pipe would likely be a hole in the exhaust, I'd be surprised if it is anything else. Condensation + leaky exhaust = moisture at startup, I'm confident that is the cause of that.
The codes are 2 digits, the first set of blinks are slower and are the "10" space of the digit, the second set or short blinks are the "1" space of the digit. So 2 long blinks followed by 3 short would be a code 23, if that helps.
As for the idle, you will probably need to re-word that for my sake, I couldn't quite get what your problem was from your description.
Your ticking sound is likely the FGS(Friction Gear Spring), which is the washer beneath the nut on the end of your intake cam shafts. It spins against the nut, and makes an awful noise that can cover up other noises! It's harmless... except for the fact that other things may go unnoticed while it continues to tap. If you rev the engine up above ~3k RPMs and the noise goes away, it's definitely the FGS. If it continues, then I'd put my money on HLAs.
Synthetic oil is almost always a good choice, and it gives you a bit longer between changes too(who doesn't like that?)
Auto trans... I know nothing about them. As for the 5 speed swap, you've already made the choice I would suggest
Strut tower bars seem to be a popular choice, just get some high quality ones! There are a few options(Corksport is probably the best bang/buck one that I can think of)
My only advice right now for buying new stuff, is to complete the car! If you're missing anything it came with originally, try to hunt it down
Oh, and a Mazda Shop manual!! I use a Chilton manual personally, but brand really means nothing. I hear the haynes is organized better than the Chilton, but I can't verify that.
Welcome to the boards, and good luck/happy building!
. some of my privious project cars ive had are 80 toyota celica supra,93 mitsubishi eclipse,a aw11 toyota mr2, a 84 nissan z31 turbo 5spd, a 73 chevy nova 350 3spd and a 84 chevy monte carlo. Im from Illinois and just bought my second mx-3 but its my first GS my first was a black rs sohc 1.6. this ones my blaze red GS. So far its got tinted windows, 18' inch wheels and tires optima yellow top battery and cone filter..(have a full header back exhaust not installed) and i love it. I am haveing a few problems with it tho. 1st of all i noticed a bit of moisture out the back of the tail pipe ..head gasket? but doesnt ever over heat and stops after hitting operating temp. 2nd is the check engine light is on, pulled codes and got the lamp to blink twice..hhmm ne-2? crank sensor? that was the only code. 3rd is after at operating temp it will idle real low like 100 rpm and almost stall out. it wont stall out unless i give it gas then let off the pedal. not sure what this is maybe a temp sensor? but wouldnt that show a code? 4th problem is a ticking under the valve covers (hla's?) it needs a oil change that i will be doing soon.. (switch to synthetic? ) last problem is hard shifting its an auto by the way. it will jurk into gear fluid is clean but smells a little burnt my plans for this caras a fun daily driver is some springs.. maybe eibach, strut tower bars, and a klde and 5spd swap! 
any info would be appriceated thanks