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I agree with @hugo7. buying new parts you mention will not improve the comfort of this ride.
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I'm not suggesting they would. Although with that stem it must ride a bit like a dutch bike. Maybe thats what you want. Also if that shim ever slips it could be painful.
Anyway nevermind, you drilled holes in your top tube now. Its only a matter of time. Normally those holes would've been reinforced.
Stem, seatpost, saddle, bars. In that order.