Migration Problems with Time Capsule and New MacBook Pro

Hopefully someone on here can help with with this problem I'm having. I just bought the new 13' MacBook Pro this week from the store and I no longer have my old MacBook Pro. I have a Time Capsule with complete backups of my old MacBook Pro and I also have the internal hard drive from it as well.
I had installed the beta version of Mountain Lion on the old MacBook Pro and the new one still has Lion.
The problem is that every time I have tried to use the Migration Assistant (and I've tried 3 times now) my files and applications are getting messed up.
iPhoto won't open. It says that it needs to be updated but when I check to update it it says that there is no update needed.
I'm seriously about to beat my head against the wall because every time I migrate the data it takes about 12 hours. I'm thinking at this point that it might be easier for me to just swap out the internal hard drives in the units because it is possibly an issue with the OS' and wait until next month to try migrating to the new drive again after Mountain Lion is officially launched.

Bob,
I appreciate your honest and prompt response. I was VERY SPECIFIC when I told the sales rep I was hoping to use the Time Capsule with two different MacBook Pro's on different subnets (one is behind a firewall on a router, one is directly connect to a WAN side IP with no firewall) and the sales rep made a point of saying that the dual band feature would facilitate this connectivity which left me with the impression (obviously wrong) that the WiFi features of the time capsule could be used to communicate with multiple Macs regardless of their own networking configurations. (I have been configuring fairly complicated networks for 20 years and only bought my first Mac two and a half years ago; the second Mac is only six months old; the third will be bought next month.)
This isn't the end of the world for me... it does require reconfiguring my network and doing a lot of port tunneling for the box outside of the firewall in order to bring it inside as well as giving up some remote access redundancies (which were based on the ability to connect to both machines using VNC software which is port specific which means that it needed separate WAN side IP addresses).
Overall I love the Mac approach compared to the nightmare that was (is) Windows (although I do also run an Ubuntu Linux box just to keep me honest). That said, your sales reps do your products a HUGE disservice when they give glib and incorrect answer to what was, I believe in my case, a very specific and precise question.
Bill Wood
Watertown, Mass.

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