Trim all white membrane and fat from the filet and chop into bite size pieces, set aside.
Dice the shallot, tie the thyme together with kitchen string, chop the parsley and chiffonade cut the basil leaves. Smack the heads of garlic on the side to break open partially and set aside.
In a small bowl mix together the olive oil, mustard and red wine with a whisk to emulsify, thicken. Add the kosher salt, red pepper flakes, herbs, garlic and finally the freshly cracked black pepper. Stir to incorporate and add the filet chunks. Cover overnight to marinate, turning occasionally if you can.
Start your grill, heat to 450°. To prepare the shish kabobs, cut the red onion and red, yellow and green bell peppers into bite size chunks and set aside.
Remove meat from marinade, reserve marinade. Start to skewer the vegetables and meat alternately until all used. Season with fresh cracked black pepper.
Grill for 2-3 minutes per side, watching carefully not to burn. Less time for rarer, more for well done. While meat is cooking place reserved marinade in a small saucepan and cook down by half. Discard the thyme bundle and garlic. Use to pour over finished kabobs and serve.