Exactly which screw have you been adjusting that you're calling the "fast idle screw"?
This page shows throttle bodies with bits numbered -
http://www.bikeboy.org/ducati2vthrottleb.html The page is about the non linear TPS reset, but the throttle bodies pictured should be pretty much identical to what your bike has and that's useful here.
Ignore the rubbish at the top in red as you do need to do an electronic reset for the linear TPS. You can do that via JPDiag, but you can also use the GuzziDiag or it's generic Marelli version called IAWDiag. IAWDiag has more options for ECU and TPS combinations that the Moto Guzzi models didn't have. In my experience the GuzziDiag/IAWDiag is a bit more user friendly.
But the numbers are the important bits to start with. For clarity, your M1000ie 2003 is a 59M ECU, PF1C linear TPS, non idle control bike. Apart from the parts about the multimeter setting of the TPS, the text on that page is somewhat relevant. You do need to adjust the air bleed screws to set the idle speed, and finish it off with the idle mixture adjustment.
On the linear TPS bikes you should never adjust #5 or #7. Lots of people do mess with #7, but #5 on the LH throttle body is more a master screw as the TPS is on the LH or vertical throttle body. The position of the RH throttle blade is somewhat set by #5 and by the synch adjustment, so make sure it has clearance and when you check and adjust the synch you might need to adjust #7 again. Just make sure, at the end of the process, it is wound in far enough that it stops the RH throttle blade from sticking shut. And has a little clearance.
But, to start with and before you do the TPS reset via the diagnostic tool, make sure there is clearance at #7 so #5 is all that is setting the throttle opening. If #5 has been messed with you need to go through another baselining procedure that the Bikeboy also sets out. But because it's in the middle and hidden generally it is untouched by the idiots who fiddle who should not.
Once you have done the TPS reset, move on to the synch. In the Bikeboy page this is below the heading "Back to the procedure", and he calls it balance. You need a vacuum tool to do this - mercury gauges, something like that. You can skip this step and assume yours is ok, but really that's just opening your procedure to another source of fail. You can pull the fast idle lever on to keep it running, and make sure you have the air bleeds screwed fully in at this point. Not tight, but until they stop.
#3 and #8 are the air bleeds. People often ask what the default setting is, but there isn't one. You wind these out far enough that the bike will idle. That is the next step. Try 1 turn out and see what happens. Go more or less as required. The only purpose of these air bleeds screws is to set the idle speed. Well, almost the only purpose.
An issue with these air bleeds is that, by definition, they allow air to bypass the throttle blades. An adjustable vacuum leak if you like. This also means that they do influence the idle mixture, as there is nothing that measures their position and changes the fuelling to compensate. Wind the air bleeds out, and you'll lean off the idle mixture. This catches people out when they wind them out to increase the idle speed, but the speed doesn't rise. If the mixture is lean, and you make it leaner by winding the air bleeds out more, it'll be too lean to increase the idle speed. So you need to adjust the idle trimmer in conjunction with the air bleeds to some extent.
Ideally, as this was all set at the Ducati factory before the bike left, the set up, if it hasn't been adjusted by the aforementioned idiots, should be "close". But you might find that you need to play with the idle trimmer to get a response. If the air bleeds are 1 turn out and it won't idle, and 1 and a half or 2 turns makes no difference, increase the idle trimmer setting. If you have access to a gas analyzer to measure the exhaust gas CO this is much easier. But if not, and if it is way off, adjusting the idle trimmer in the diagnostic software will either make the RPM rise or fall. 1100 - 1150 RPM is a nice idle speed.
If the idle RPM rise by richening (or leaning) the idle trimmer setting only, then that means it was off. Set it so you get the highest idle speed, then if that is too high, go back and wind the air bleeds in to lower the idle speed. Because winding them in richens the mixture due to reducing the air entering the engine, you then have to lean the trimmer setting off. It's a bit of back and forward if the bike is a long way off, but you should get to the point where it is happy. If you have access to a gas analyzer and can read the mixture at the muffler or, ideally, in each header, it's much faster and accurate. Maybe ask an auto shop if no bike shops near you have a gas analyzer. Smog testing places should have one (depending on your area), see if they'll let you have a play. I'd go for 3 to 6%, 5% if you have time to get it really nice.
Generally, the idle trimmer setting will be between -10 and +20. Really, 0 to +15 is the range you "should" see if everything is "right", as this is all part of the set up procedure the Ducati and Marelli engineers went through when they developed the mapping, and I believe they usually started with the idle trimmer set to 0.
How right you can get it will depend on the tools you have to hand. Doing the idle trimmer setting by ear you'll find a pretty wide range between hearing the idle RPM drop at the lean end and again at the rich end. Try to pick those points, then go the middle. You can also adjust the idle trimmer setting to give nicest running at low speeds and cruise and fuel economy. If you're prepared to play with it, and make adjustments of 2 or 3 points at a time, you should be able to make it a nice thing. Be patient.
And it should start easily. You can also play with the mapping using the GuzziDiag flashing tools and TunerPro if you really want to get stuck in.
If it only has 3300 miles, I'd do a fuel filter and clean out the tank to make sure it's not gunky or rusty inside. Give it a good dose of Seafoam or the like to clean the injectors and do some miles with enthusiasm before the idle setting to allow it to clean out if it needs to.