Definitely use the same thumb slugs in each ball if you want to compare apples to apples. Also, know the difference between urethane and vinyl slugs. Urethane are slicker, vinyl coarser.

I would strongly suggest you have your driller install a switch grip system. This will allow you to experiment to your hearts content without redrilling each ball with what you THINK is the perfect pitch only to find out a few games later that it isn't. I went through years of redrilling a dozen balls at a time whenever I thought I'd come upon the perfect pitch combination. The fact is, what feels good now may not in a few days, weeks or months. The switch grip will allow you to drill just ONE inner sleeve (a removable thumb slug) that will fit in all your balls fitted with a switch grip outter sleeve. The beauty is that if you drill the hole in your ball to accomadate the outter sleeve at ZERO PITCH it will allow you to alter the inner sleeve pitches up to 1/4" lateral, foreward or reverse.

With the above stratagy you could drill several inner sleeves at different pitch combinations (as well as sizes) that can be used over and over again. I use 1/4 left and 1/4 reverse when I want to get out of the ball sooner with maximum axis tilt. I use 0/0 pitch for my normal shot and 0/1/4 forward on those days when I want to go straight through the ball and have my thumb come out a bit later (or to totally relax my arm swing).

The switch grip will save you money in the long run, reduce the need for tape and provide many options for tweaking your pitches (and even your span up to about 3/16ths of an inch).

One more thing, it's not unusual nor necessarily an indication of a poor fit or improper pitches to develop blisters initially (and I stress, initially). Give those sore spots a few days to heal and your thumb a chance to toughen up in the areas that are prone to friction. If blisters keep reappearing then, yes, your driller needs to adjust your pitches and/or span.