Thanks for e-mailing.
From the pic you attached, it looks like you have the factory Yamaha coils from the 1979-and-earlier "points" model XS650. A pair of single-tower coils is what you'd use with a "single-fire" ignition system ("single-fire" meaning that each cylinder has independent spark, timed to only its own compression stroke, every two crankshaft revolutions - no "waste" spark on its exhaust stroke).
A single-fire system is what I always recommend for built engines, and an 1180cc XS650 twin would have to qualify as "built," in my book (is all that displacement obtained only with a bore increase, or do you also have to stroke the crank to get there?).
In theory, a "dual-fire" system (one coil, two spark leads, both cylinders receiving a spark each crank rev) will work in a 360-degree crank engine, and it did work pretty well when the factory switched to it in 1980 and beyond. The rub comes when you start hotting up the engines, especially when you fit aggressive longer-duration, higher-lift camshafts; then the waste-spark begins to create problems. So, single-fire is what you want.
The Probe Engineering, Inc. Model XS-65L ignition is our single-fire system for "standard" (not rephased) cranks. I have attached a PDF file of the installation instructions for you to look through; the pages of interest as they relate to some of your questions start on page 11 (see steps #67 through #70) and page 13 (Appendix 1, covering the rev limiter). You might want to look over those pages to help clarify what I'm going to describe below to answer your specific questions.
1. Starting - at all crank speed from zero RPM through 480 RPM, the ignition fires in a dedicated "start" mode. In start mode, the spark is retarded from the full-advance setting by 30 degrees of crank rotation. For a monster-displacement engine like yours, with what I expect will have a moderately high compression ratio, as well, I expect you'll be running full-advance timing in the range from 30 degrees BTDC to 35 degrees BTDC. If you end up, let's say, at 32 degrees BTDC full-advance timing, the retarded spark in the 480-RPM-and-below start mode will occur at 2 degrees BTDC - nearly TDC. I have a built ironhead Sportster (10:1 Wiseco pistons, cams, carb, exhaust, headwork) that is kick-only, and the ignition on that has the identical setup to what I'm describing here, and at(a now-svelte) 165 pounds, I can kick it to life without fuss. My kick-only bikes are, in fact, the reason behind the Probe "start" mode design, and that inonhead is among the toughest examples.
2. Above 480 RPM (that is, once the engine's running on its own, and not being cranked by some outside mover), the ignition is in the "run" mode, and the electronic advance curve determines the spark timing. That advance curve is defined by three variables; the first is the full-advance timing, the second is the idle-speed timing, and the third is the engine speed at which full-advance timing is reached. In the "standard" XS65L system, two of those three points are under your control, and are independent of one another; the full-advance timing and the idle-speed timing. Full-advance timing is set in the familiar way, by rotating the back plate assembly that carries the timing sensors (Hall-effect devices) up on the cylinder head (located in the left camshaft end housing, where Yamaha put the points in the early engines). The other end of the curve, idle-speed timing, is electronically adjustable, (that is, while the engine is running, and without physically moving anything) using two micro-push buttons that actuate a solid-state potentiometer in the Probe control module's timing circuit. Using this adjustment, you can set the idle-speed timing anywhere in the range from a couple of degrees ATDC (yes, After TDC) right up to your full-advance setting, in 64 discreet steps. The potentiometer has non-volatile memory so it stays where it's set even powered off.
3. The third point that defines the advance curve, the engine speed at which full advance is reached, is not normally user-adjustable, and is set to 3,000 RPM when the module is programmed (programming takes place prior to potting the module guts in cured epoxy, and the programming terminals are not accessible after potting, so it's not re-programmable after completion). I have found this to be a good figure for a wide variety of engine builds.
4. Rev limiter - page 13 of the installation instructions details the available rev limiter settings (including a rev-limiter "defeat," which we don't recommend, but some guys think they're exempt from the physics of metal fatigue). With a stock 74mm stroke, 4,000 ft/sec linear piston speed, the usual "don't exceed" stress limit, occurs at 8,238 RPM, a little above the factory's conservative 7,500 RPM redline. 4,400 ft/sec piston speed, a sometime "peak" heat-of-battle short duration limit for racing, comes up at 9,062 RPM at the crank. So, you can see that available rev-limit settings cover everything from the mild streeter to blood-in-the-eye racer (and again, those with brass balls can turn it off entirely).
NOW, I'm going to veer away from a strict description of what the XS-65L system is to other topics.
First, your coils - the coils in the pic. If these are OEM coils marked CM11-50, they have 8.6 millihenries of inductance and 4.2 ohms primary resistance. Without boring you with the math, that means they store 35 millijoules (mJ - a measure of energy) at 12 volts. That is the lowest figure (tied in last place, actually) of all the coils I have measured, and not by a little bit, but a lot. In my big Excel coil-comparo spreadsheet, "good" coil energy ranges from about 67 mJ up to 116 mJ, so the OEM coils deliver about half the energy I'd expect from a decent part - and that explains why they were panned even back in the 1970s, and even on stock 650 twins. No matter whose ignition you use, I most strongly recommend you bin those coils and fit new, quality aftermarket bits - your built engine will need them. I can provide specific recommendations, and no, I'm not in the business of making or selling coils, so I've got no financial interest in this bit of unsolicited advice.
Second, after you've digested what level of advance curve adjustment is available to you in a standard XS-65L system, if you conclude that you'd also want other options on the full-advance engine speed (recall, that's baked into the cake when the module's programmed here at our factory), I DO offer custom-programming services, and a module could be programmed to give you alternate full-advance engine speed settings (say, starting at 3,000 RPM, and going up in 250-RPM or 500-RPM increments to some higher figure). To do this, however, means "re-purposing" two of the three toggle-type DIP switches that are normally used in combination to select from all of those rev limits. That doesn't mean you could not have a rev limiter; it does mean that you'd have to specify your desired limit up front, and it would not be adjustable, though it could be "defeatable" (you could override it, for no limiter). There is an extra cost for custom programming, which covers the both the programming proper, plus revising the installation instructions to reflect the changes and archiving the design (and instructions) changes so that the whole package is supportable and re-creatable.
Well, my fingers are wearing out, and this is probably a lot to absorb, so for now....
Probe Engineering, Inc.