Cuts out after a few miles, spits and sputters

Hello all, new RSVR owner here. Second Aprilia.
2004 Aprilia RSV1000R
4500 Miles
Akrapovic race cans
PC3 installed
Brown wire mod completed.

Bike starts and idles just fine. Warms up and everything is great. I test drive it down my street and back and it has all the power expected of it, no hiccups or sputtering. I take the bike for a longer test ride and after a few miles it starts to sputter while riding, and sometimes completely dying while riding. Once the problem starts it doesn't go away. Every gear, every speed. I say every speed even though it doesn't give me the chance to get up going fast because of the jerky spitting and sputtering.

I have changed the map on the bike via PC3, I did the longer test ride, seems like I got further this time around. But it still ended up sputtering. Very embarrassing on a sexy bike.

I have checked:
All ground
All wire looms for shorts/ bare wires
Changed the spark plugs
Verified the air filter is clean, oiled, and seated properly <weird air-box with no cover/I guess the gas tank is the cover
I have added ground wires the frame and to the engine for whatever reason
Using the PC3 I reset the TPS to 0-100, was maxing out at 83

Test drove it again, got much further, alas, its fixed, on the way back..... she starts acting up again.

Things I believe I may need to check:
Fuel pressure- Dont have a pressure gauge
Injectors- Dont have a noid light
Fuel filter- I will remove and visually inspect/ havent done this yet

I did want to mention that the air intake door appeared to not be opening. I wedged the door open and disconnected the hose to the control valve for the door. The bike went further when I did this but still ended up having the spitting and sputtering.

PLEASE PLEASE PLEASE HELP

Thanks for the fast reply, did fuel pressure test today. Had nearly 50 psi. However I wish I could do the fuel pressure test while riding. It is so strange that the bike starts acting up after a few miles of riding but works like a champ until then. Got it to 145 today with full throttle response, a few miles later, sputter sputter. Got it back to my shop when it was running well but by the time I got the tank lifted the bike was having proper throttle response again.

Checked the resistance of the plug wires today: front cylinder plug wire has 5.02 ohms, rear cylinder wire has 5.85 ohms resistance. I asked a friend he said thats okay, as long as its not 2, 3 or more ohms over/under spec. Still testing and checking things. Ideas are greatly appreciated. I did the side stand switch bypass and that didnt fix anything. Im gonna end up in an insane asylum soon if i cant fix this bike :cuckcoo

Finally decided to pull the tank. I found a filthy fuel pump sock,

cleaned it

then checked the fuel filter, I could barely blow thru the filter. It was extremely clogged. So I purchased a WIX 33012 for around $10 and some fuel line and hose clamps.

This fixed the problem with the bike spitting and sputtering after a few miles of riding. My problem now is a low idle. Whats happening is: at idle, if i blip the throttle, the rpm's go down a little bit before going up, but most of the time the bike will just die. Or when I'm riding and I down shift, if the bike hits idle for more than half a second it dies.
I am using this PC3 map: "908-519 European Model-, Akrapovic racing Slip Ons, Stock or aftermarket air filter, Stock ECU set to Map 2 (race mode) by Aprilia dealer"
Is there a better map for my setup and I'm not seeing it? I just purchased this bike from a 3rd party which knows no details about the bike :confused

not sure, new bike and no details from 3rd party seller. I was going to ask my friend to do the throttle body sync, how is a co level checked?

Thanks Jonny, I reset the tps by using the pc3. The max was only getting 86% so i reset it so that max/wide open throttle is now 100%.

Had to get it towed in last night. :angry Bike was riding fine, parked it and went inside, came back out roughly an hour later and bikes not working... It cranks over and even sometimes starts, but it sounds like its starving for fuel. I can hear the fuel pump prime when I turn the key on. It has a very low idle and the second you give it any throttle it shuts off. After trying to start it about 10 times I gave up and decided to lift the tank to see if there was an easy fix. Nope, no hoses pulled off, no leaks anywhere, no melted wires. I then did the diagnostic thing where u hold down the lap button and got no codes. I also checked the fuses up front and the two 30amp fuses, all were good. Any ideas anyone? :confused

Update: Fuel pressure test shows only 10psi. Replaced the pump today and rode it home. Hope that is the last of my problems!