I need to know if I need to replaace my axles or not when doing a engine swap? And how much does a wiring harness cost? And lastly how much does a transmission swap cost? I want to change from a automatic to a standard? Any help would be appreciated. Thanks..

It's good to change the driveshafts when they're out anyway, but you don't have to. What engine are you putting in what car? You won't need a wiring harness unless you're doing a crazy swap like (1.6 - 2.0).

Swaping an engine is no picinic, man. The big question is whether this is your day to day car, or if this is your toy.

If it's your day-to-day, avoid thrills and reuse whatever you can. The only reason that driveshafts will really crap out is if the boots are torn. Even then, joint replacement kits are available, and you don't have to replace the entire axle.

A 5-speed tranny isn't cheap either. At least $500, since you want a low-mileage one. Higher mileage trannys tend to exhibit 5th gear popout, and the entire thing needs to be rebuilt. The shifter, linkage, and shift bar can be picked up from a salvage yard for less than $100, I would imagine. the car and engine will accept either the auto or manual, so no mods have to be made to make it fit.

Beyond these things, you have about a million other things to consider. You'll find this site indisposable as you progress.