The two models you say you would "like" will most likely lock you into a "Remlin". A standard blued Jm in .357 have become very hard to get let alone a stainless one to use for a platform to build what you want.
Talk to a local gun store nad explain your situation. Tell them you want to order a CSBL or CST but if it arrives with crooked sights or any other issues that you are sending it back and trying again. Or attend local gun shows until you find one that is acceptable. Once you have that you than can begin your search for a gunsmith to have what you want done to it. Smoothing up a Marlins action and improving the trigger and hammer is not custom work nor does it make it a custom Marlin.
To me a custom Marlin would be buying a JM 1894 in rough shape and sending it off for a new barrell, new wood and new finish in the caliber I wanted. Add any other bells and whistles like large loop and scout rail and sights ect... Probably require a $5k budget.