I've used a couple of soft scope apps, they got me in the ballpark for the most part...but I agree, an analog scope is much better. Something about how an A/D interface messes with the input signals going to a soft scope that just doesn't work as well or as smoothly or as accurately as a hardware scope.
I picked up a decent quality and in good shape Tektronix scope on eBay for like $125.
Then I got brand new probes and assorted options from a Hong Kong seller for like $15...?
For less than $150...I have a nice/flexible scope that really does the job well.
Here's an interesting/puzzling consideration….
When I was talking to some guys on another analog/tape forum awhile back...one of the guys made a good case for NOT doing the azimuth or especially any of the other physical adjustments to the heads (tilt, etc)unless the deck was new it it was the first setup or if you had the heads relapped and/or were completely replacing them.
His point was that once tape starts working the heads...it creates a path, and if you do physical readjustments...you keep changing that path which may actually mess up the head's performance and subsequent electronic calibrations.
He felt that only the electronics should be adjusted once a deck has been broken in. His logic was that the heads or the screws that hold them won't move on their own so no need to physically readjust them.
I don't know...everyone seems to always do the azimuth with each calibration, even if they don't mess with the other physical head adjustments...but the guy make sense.
Like...if the used heads DID somehow get physically wacked out of position...how the heck to you find that pre-worn "path"...if the azimuth adjustment makes the tape ride off the path...???
That said...on may last calibrations that I did end of last winter...I did the azimuth anyway on both my 2-track and my 16 track. The 2-track was basically a brand new deck, so it was not problem, and the adjustments ended up back exactly where they were set at the factory...so that supports the "screws don't turn on their own" theory.
With my 16-track...it's older and has seem some use...but it's not worn, and even with it, the azimuth ended up in the same physical spot as where it was originally. (In both cases, I marked the positions of all screws with a fine-point marker...that way I know where things were before I messed with them.

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Alan...sweets is right...before you get to the MRL tape stage, there are a few steps you need to do just to set up the MRL calibration process. A service manual for the MS-16 would be best or at least a generic step-by-step guide.
With calibrations...EVERYTHING depends on the initial setup before you spin tape...otherwise you end up calibrating against a bad reference point if you skip something or don't get that starting point right....or don't follow the proper sequence of the whole process.
Here's some reading and viewing material for the weekend...you will see there is a basic processes, but also some differences in how each person does it:
(Keep some Advil on hand...you WILL get a headache, but once you start to unravel the process in your head...it's not too bad.)
http://www.sonicraft.com/a2dx/Analog_Warriors.html
http://www.johnvestman.com/alignment.htm
https://www.youtube.com/watch?v=JW5kifLh598
https://www.youtube.com/watch?v=MUMtN2kQtqw&feature=related
http://www.analogrules.com/basicalign.html