OK, long answer, but many things going on here!
So it sounds like what you are trying to achieve is to run a full-sequential setup, correct? Normally you only need the one trigger (such as the 60 minus 2 off of the crank-trigger) to make things happen in a phased-sequential/batch-fire setup, but you are trying to use TWO triggers! Why? To run full sequential?)
Why else the 2nd trigger?
1) Are you using the hall-effect trigger in addition to the crank 60-2 because you want to use that 2nd signal to trigger the sequential fire? Dunno if that is how it works with the M48, but clarify that (for yourself more than anything) and verify those settings.
2) If this is the case, I doubt STRONGLY that they would recommend application of the stock single coil for it! With our most basic installation we use the base-model GoTech Standard for example and there we keep the stock single coil and the system simply triggers coil-fire-direct to the stock single coil (and then via the dizzy that now simply sits there and becomes a dumb-device to only distribute the spark via the GoTech's commands!)
Our Standard model harness has a connector that plugs right in to the little blue hall-effect sender on the side of the stock Alfa dizzy. However, this remains a batch-fire scenario as mentioned and we don't need the crank-pulley 60-2 trigger mods! In this scenario, that single stock coil is firing for each of the plugs and the distributor is simply doing that - distributing the spark based on the ECU's commands.
3) You can try it with the M48, but this was the reason for my question in point # 1 above; if you are trying to run this in a full-sequential mode, I strongly doubt that the stock single Alfa/Bosch coil has the duty-cycle to be up to the task! (This is likely why it is getting hot!) Also, with our basic Standard version box we need an ignition-module (such as a TP100) to drive low impedance injectors. With high impedance injectors we don't need the ignition-module. (Also with our middle "Pro" and higher models discussed below, we don't need an ignition-modue when running low impedance injectors...) Verify the comparable issues/guidelines with Motec on your installation.
4) In a more advanced installation of these types of systems, where you have converted the crank-pulley to a 60-2 setup, you can typically drop the distributor! Pull it out, lock the oil-drive with a nut and washer and cap-off the old dizzy hole! Now you have a 60-2 crank-pulley trigger-wheel and magnetic crank-angle sensor to drive the signal and that is all that you should need! In this scenario though we would upgrade to the middle-child GoTech Pro for example and there we have to run some new stand-alone coils too. Also, on a V6 we would still fire it batch/phased-sequential (just like a factory system), but now with multiple coils (one for every two cylinders!)
Now we use a coil-brick consisting of say 3 x 2 double coils such as the Alfa 155, VW VR6 etc. Essentially just 3 coils - each with two plug outlets - and we fire those sets of coils in phase! We'll first fire the coil that has plug-leads to holes number 1 & 5 connected to it, then we'll fire the coil that has leads running to hole numbers 3 & 4 and then the coil that drives spark plug numbers 2 & 6 and then back to the fist coil again (to meet the standard 1-4-2-5-3-6 firing order and also batch-firing the associated piston-pair with each phase!)
I don't think that you can achieve this with the stock coil - especially not if you are trying to run full sequential! That coil can never keep up - it doesn't have the charge-time or the power!
5) Again, not certain about your Motec world (I can only equate things back to my GoTech world here and hope to help you); if we really want to run FULL sequential, we need TWO triggers and on a V6 (or higher cylinder car), we have to move up to the top GoTech Pro-X model! (Now we can run 6 individual COPs!) In this installation we would still trigger the box with the 60-2 crank-trigger for example, but for the full-sequential mode we have to now also add a second trigger - typically off of the cam that only turns at half-speed!
Here too - verify what it is that you are actually trying to achieve! Naturally for this type of installation you need 6 individual coils with 6 individual plug-wires, or 6 coils directly on the plugs (COPs) as mentioned before! Now you'll actually fire those coils individually first number 1, then 4, then 2, then 5 and so on.
6) There is a basic "test" that I perform early on in an installation with our systems! (Perhaps it's easier for us, because we have fuel and timing trigger signal LED lights - right on the front of the ECUs!) Do not know about the Motec.
Any way, I can have a harness COMPLETELY out and uninstalled from the car and ONLY plug in the crank-trigger signal wire (or the hall-effect signal wire - in the event of a hall-effect sender/distributor installation!) I hook up JUST the ECU's main power supply - even to a battery seperate from the car - I just power the box and give the loom signal from any random rotating magnetic pickup! I crank the motor over and the LEDs on the box will flash! If they don't, I go hunting for a signal-issue with my trigger!
Either way, sounds to me that at least 3 individual coils is where you are trying to be. (At a bare minimum, if you are doing a batch-fire install, upgrade to a better/newer/faster coil!)
