I do just fine rolling from a kneeling postion, but when I go to do it from a standing position I either freeze up or I get so stiff I do it completely wrong. Also they have me on some medications that work on the pain and inflammation of my collar bone, but even with them it still hurts just a little. Oh yeah I should also point out that I am 6'5" and I weigh about 310 so it is kind of hard to become really flexible and become like a ball.
I guess it depends on how long you've been doing this - seems you're quite new. See if you can practice kneeling ukemi (forward and backwards) at home, on the lawn, on the mats before practice for a few minutes to start with and work up to 10. Start also to do back/side ukemi from standing. At first, only go to the back and rock back to the feet - when you get more comfortable at doing this diagonally across your back (from, say L hip to R shoulder) continue this on to a full back roll. Eventually work to pushing your way back to standing from the back roll. By this time you should probably feel safer or more confident about attempting some forward from standing, but also enlist the help of a more senior student...
I know heaps of people who are 6'5" (not in Aikido - I work at the national rowing federation here in the deeeeeep south), but they don't weigh as much. (we have a couple of 6'7" 230 scullers who can crank out 2000 m on a Concept 2 rowing machine in less than 5:45 - if you can do that, I'll suggest you contact someone named Mike Teti, about the US team for the 2012 Olympics in rowing). With time, practice, and the "push away" (from the table) exercise, your weight could come to the 250 range if you're relatively muscular, or less if you're not very muscular. Probably in a year or so you'll wonder what caused you the worry.
I apologise if I've assumed anything about your body composition, but it may also pay to spend some time doing push-ups, weights in general, abdominal/core work over and above the training you do in Aikido. There are "rubber band" and weights exercises you can do to rehabilitate your shoulder/rotator cuff so that the whole structure is more resistant to injury, also - just about any fitness club should be able to show you those, or you can hop into Barnes and Noble (or similar) and scan through books on strength training. Another GREAT exercise is swimming - no shin splints, but your shoulder will need to heal before you do that.
Hope you get over the fear soon - a well executed roll from a big guy is a good thing to see.
Oh.. The pain (leaking through the medication) is probably a sign that you need to spend some time healing rather than repeatedly re-injuring.