I think comfort is the pre-requisite factor in deciding to buy a bike, and only you can decide that. If stem and bar modifications make the bike comfortable then that's great. It took me two replacement stems for me to be truly happy with my bike - I found a long low stem whilst lightening the front slowed the steering down too much and gave me back ache. I finally settled for a short very upright stem (70mm 17 deg) and 2" riser bars. This gives a more upright position than many would recommend but I find it comfortable, and steering is quick and responsive. You might find a shorter higher position better.
Your back and shoulder muscles will adjust a little with riding, but don't get something that is truly uncomfortable to start with.
Richard
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Currently riding an MTB with a split personality - commuting, touring, riding for the sake of riding, on or off road :)