How To Switch To A Higher Storage SDHC Card With Less Hassle And Problems?
Multiple questions in one, so let's see how to address them:


if those issues you report already happen with the "old" card inserted, they probably won't get worse with the "new" card (if they are card-related at all) -- so I would not connect these two. Though I had that #1 problem with a certain card (but not with another), after a ROM switch (replaced stock by Cyanogen) the problem switched as well (lucky me, now the new and bigger card had no problems anymore) -- so there might be certain compatibility issues, and switching cards could even get you rid of that FC problem. But mostly, such FC problems are rather solved by cleaning the cache of affected apps, or (worst case) doing a factory reset. If your device is rooted, wiping the Dalvik Cache (an option available with enhanced Recovery) would be an alternate approach to the factory reset, in case the Dalvik Cache got messed up.
the market issue should not be related to your SD card either. Here it may help to clear the market cache (via apps->manage apps).
concerning your .apk, the solution could be provided by apps like AppMonster -- which creates a copy of .apk files from installed apps to your SD card (the Pro version even does so automatically on each install/update, so you can easily switch back to any previous version of an app when the latest version shows problems).
keeping the old card for a while (leaving it untouched) never can hurt, as it provides another backup :)