I take it you are using the XS1100 carbs because you already have them? If you have not bought carbs already go with the FZR1000 or similar as they are down draft ( 45degreeangle). I'm using keihin flat slides and they clear the master cylinder no problem.. Using pod filters the side draft style bike carbs would likely clear the master as most are mounted very close to the cylinder head.
What ever style of pedals you opt for will need fabrication in order to mount them, I'd prefer the existing location for a variety of reasons. $150 isn"t enough savings for me to,warrant the extra work to switch to,floor mount pedals. I've had them on couple of single seat race cars but those were designed with them................... if you already have the XS carbs it would be cheaper to sell them off and get down drafts then to redo the masters.

Tom