Engine 94 Cobra

+1 to mr. addermk2, on all counts. I self-tuned my '95 Turbo and he describes exactly what I went through (without the steep learning curve). With a wideband O2, a good datalogging chip, injector parameters, an MAF transfer, and knowing what the heck you're doing (not impossible but not easy to figure out very quickly), you can make a heavily modified car run as good / better than stock, have it pass emissions, be completely street-able, make more power, and live a longer life. Or you can pay someone skilled and experienced to do it remotely, time is money after all.

I'd only add that I consider "mail order" tunes (a best-guess Bama tune for example) and remote-tuning (what addermk2 describes) very different - maybe the source of confusion here. I'm also unimpressed with the shortcuts (and high prices) of dyno tuners in my area. Time is money - I've heard of them updating the tune's displacement rather than fussing with new injectors, which completely throws load calculations, timing, and everything else under the bus.

My order of preference is DIY (for those who have time, patience, and technical skill - also not cheap in itself as a QuarterHorse with BE ends up being around $350), remote-tuning by a skilled person like addermk2 or decipha I've interacted with on these boards (and who have educated me a few times), a canned mail-order tune, followed by dyno-tune, followed by nothing, followed by swapping to a carb, followed by selling my car, followed by a GUFB swap. :)
Yeah when I was thinking mail order tune I was thinking something along the lines of Bama and the likes. Would buying all the stuff needed to self tune be worth it for the guy who doesn't change combos often and has the same set of heads for 10 yrs and doesn't race nation wide where one would need to make adjustments due to weather and altitude? Ehh I dunno.. Can you elaborate on "updating a tunes displacement"
 
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That's where people benefit from my service. Updating a tune for an altitude change is simple... and if you recreate those conditions during the initial tune, it's all covered.

I've also got a lot of historical data that gets used to build temperature compensation into the tune.

When I first tuned my 351, it was 78* ambient. I fired it up yesterday while it was 21* outside. Cranked first time and idled smooth.

It's all about attention to detail.
 
Yeah when I was thinking mail order tune I was thinking something along the lines of Bama and the likes. Would buying all the stuff needed to self tune be worth it for the guy who doesn't change combos often and has the same set of heads for 10 yrs and doesn't race nation wide where one would need to make adjustments due to weather and altitude? Ehh I dunno.. Can you elaborate on "updating a tunes displacement"

That's a really good question. I guess it depends on what you like to do. It takes some time to get the hang of things, but for someone good with computers and who enjoys sitting in their car with a laptop and looking through datalogs working towards a perfect tune, it's a great deal of fun. I really like having complete control over every aspect of engine performance without having to buy a thing (as you would for a carb'd car). Change jets, change timing, change the timing map, enrich, lean, accelerator pump, power valve, WOT fuel, idle speed, shift-points and pressures, it's all completely in your control. I'm always tweaking something on my old pile, so for me long-term it's cheaper than paying someone.

On the flipside, if you hate technology, but just want a turn-key smooth-running car putting out great, safe power, it's easier to pay for it. With enough time I think you can eventually land in the same place either way, it just depends on how much you enjoy getting there. If you consider your car largely "done," and don't plan any more changes, it might be better, quicker, easier to just have it done for you.

The only thing I'd say for altitude changes is that theoretically the stock tune is already set to compensate. Mass air is mass air as far as it's concerned, and there are altitude tables for spark as well. If you're getting driveability issues because of the altitude change, you might benefit from having a pro tuner take a look to see why. Or taking a look yourself.

If I were you, and I decided I might benefit from a tune, and this sounded like fun, and I felt I was technically skilled enough to figure it out, I'd get a Moates Quarterhorse, skip the Binary Editor and instead use Tuner Pro RT (I posted a few weeks ago how / where to get that). I'd see what I could see on my own, of course with the help of folks on this board.

If that doesn't work out, or if it's overwhelming, you're really not out anything. A lot of the professional remote-tuners will perform their services on an existing Quarterhorse.

This is a great guide to give you a beginner's understanding of what's involved. http://www.v8mustang.com/Getting-Started.pdf

p. 15 of that document talks about the hack of setting the Engine Displacement parameter in the tune instead of setting injectors and MAF transfer values. It's basically a sketchy shortcut pro dyno tuners have been known to take.