Should I start from a base car if stock parts are gonna get upgraded anyways?

Giving up on the fruitless endeavors of an alternative swap besides an LS (car in question to be a New Edge Mustang). Would plan for the following things:
 

• aluminum 5.3 LS
• 31-spline 8.8 (are Mosers on the affordable end?) and am undecided between the Detroit Truetrac unit and the Torsen T2R
• Subframe connectors, PM3L conversion, at least 1 or both of a panhard bar/torque arm, and Cobra brake parts
• Must have a manual, so I plan on having the TR-3650 (have heard that there is an adaptor to connect to an LS + way cheaper than a T56 option)

So am I better off starting with a base V6 car since a lot of these parts would have to be replaced anyway, or is a crapped-out GT more simply to start from the getgo?

I'd say it depends. The parts you pull out of a clapped out GT are likely to be easier to sell off for more money than those from a V6 car.   While finding a V6 manual car is possible, they aren't as common as V8 manual cars, unless you are OK with entirely reworking a clutch pedal mechanism.   What is the end goal for the car?  Street car or dedicated track rat? I.E. - what level of civility will be required? 

In reply to Ian F :

Refined, but raw - would only hit the track once a month

Also:

https://orangecounty.craigslist.org/cto/d/anaheim-2003-ford-mustang-5-speed/6839220782.html

https://inlandempire.craigslist.org/cto/d/moreno-valley-2004-ford-mustang/6825506248.html

https://losangeles.craigslist.org/lac/cto/d/lynwood-2004-ford-mustang-40th/6837073639.html

https://losangeles.craigslist.org/lac/cto/d/los-angeles-ford-mustang-v6/6829948209.html

I'd say find a v8 car because they're so cheap anyway and almost purely so you'll already have an 8.8 axle.

The tr3650 to ls option does exist and I just looked it into as an option for my GTA. The tr3650 has an integral bellhousing. The adapter setups replace the front half of the case with a front cover with a mounting flange for a 4 bolt wide GM style bellhousing. You then need to source a bellhousing. 10 spine clutch options seem to be a bit thin so you might want to swap to a 26 spline input shaft while you have the trans apart. The point where I decided it made more sense to hold out for a t56 or a tko500 is in there somewhere but I forget where exactly.

Also. Unless you are really attached to the look of the new edge, sn95s are cheaper and effectively the same for your purposes.

Daylan C said:

I'd say find a v8 car because they're so cheap anyway and almost purely so you'll already have an 8.8 axle.

The tr3650 to ls option does exist and I just looked it into as an option for my GTA. The tr3650 has an integral bellhousing. The adapter setups replace the front have of the case with a front cover with a mounting flange for a 4 bolt wide GM style bellhousing. You then need to source a bellhousing. 10 spine clutch options seem to be a bit thin so you might want to swap to a 26 spline input shaft while you have the trans apart. The point where I decided it made more sense to hold out for a t56 or a tko500 is in there somewhere but I forget where exactly.

This.

Then I'd just beat on the stock engine until it pops while you gather parts.

In that case, the $1100 one looks perfect for your needs. 

As someone who has a LS swapped New Edge I would recommend starting with a GT.  It has bigger brakes, bigger sway bars, 8.8 rear end(most with LSD already).  The V6 car doesn't come with a 8.8, they have a 7.5 to the best of my knowledge.

The TR3650 adapter and upgrading to a 26 spline input is not a cost effective option otherwise I would have done it.  I started with a Tremec TR6060 but ran into vibration issues from not having a slip yoke.  I'm now using an Aisen AR5 from a Chevy colorado/Pontiac Solstice with an adapter plate from FabBot Fabrication that uses a modified 4L60 bellhousing.  The whole setup including transmission was under $1000.

A problem you will run into on the New Edge is making gauges work.  On the older SN95 cars they had analog gauges so you could run dual sensors in the motor.  The New Edge gauges run off a canbus network and won't work.  You could possibly leave the 4.6 computer in the car just to run the gauges but I haven't tried.  I have done that on a Corvette.  I'm running a Racepak so the gauges are not an issue.

Another thing to consider is what you're going to do with the car.  Not many classes outside of drag racing are friendly to LS swapped Mustangs.  In SCCA you're limited to CAM or SM.

If you planning on shelling out the money for a aluminum 5.3 you might as well consider a Coyote swap as an option.  You can keep the 3650 going that route.  A Coyote truck motor can be had for less than $2k.

In reply to Patientzero :

Have the coyote engine swap tuning problems been reliably solved?

In reply to Floating Doc :

I've done multiple Coyote swaps into various vehicles and I'm not aware of any tuning problems utilizing the Ford Racing Controls Pack.

In reply to Patientzero :

Where?  Last I looked, locally they were $4k+ engines, which is weird for a new vehicle - normally they are low because there is a lot more supply than demand.

If your going to throw that sort of parts list into the car why not just find a nice Cobra 5.4 and call it a day. You can run in a lot more classes and it will have value at the end of the deal. Bet it would be cheaper in the long run. 

In reply to wearymicrobe :

I didn't think 2000 Cobra Rs were growing on trees. A 4.6 Cobra is definitely a solid suggestion though.

Edit: actually looks like even naturally aspirated New Edge Cobras are into 5.0 S197 territory.

In reply to Knurled. :

LKQ or car-part.com, with a warranty.