SSD is different, it needs a separate driver from OS to work properly. It is better that you archive your drive using time machine, install OS X as usual and than, during the last install step, restore your home directory. This will ensure that your system uses all correct drivers and your SSD will live a healthier life.
When archiving with time machine, you can drag /System into the exclusion list to avoid archiving OS X itself (you'll be reinstalling it).
TrueCrypt 7.1a has gone through at least two audits. They found a couple of high-severity issues were found, but there are no known exploits against them, and one only affects the Windows version. And the one that affects Mac OS, like many exploits, requires physical access. Unless you are worried about your macbook falling into the hands of the NSA or Russian hackers (note: I'm being hyperbolic), I wouldn't be too worried. I'm pretty concerned about security myself, and I'd have no problem using TrueCrypt. The only concern I would have is future compatibility as operating systems evolve and drop support for older stuff.
But there are two active forks off of 7.1a, only one is ready and stable, and has a Mac version: VeraCrypt.
Once you set up an encrypted volume - essentially a loopback file - you still have to format it with something cross-platform. I'm guessing you already understand this part, but if not, this is going to be your biggest cross-platform issue. Or at least, it has been for me having done this kind of thing many times.
FAT32 is really the only rock-solid cross-platform filesystem. It comes with a so-called 32GB partition size restriction, but this can be overcome, for example with Fat32Formatter.
NTFS "should" work, in the form of NTFS-3G, but in practice it never has for me! This could be just my experience, but every time I've tried it I've had issues: either lost data or had concerning enough file integrity issues that it worried me too much to trust important data with. NTFS-3g claims that they comply with NTFS rules better than Microsoft, and that any integrity issues that arise are Microsoft's fault. Which seems plausible to me. But the bottom line is that whenever I used NTFS-3g on a volume, then used it natively in Windows, it had oodles of integrity issues using Microsoft chkdsk. And like I said, I've lost data before, more than once. Personally I just don't trust it.
But in the last few years, I've not had to worry about cross-platform issues. Because, if I need to use NTFS from Mac or Linux, I just use it natively in a VM and share it via CIFS. I've even used Windows 2000 (with no licensing issues) in a VM to access NTFS volumes from Mac or Linux.
But any more, the only "cross-platform" file system I use is ZFS. I used to use two small 1tb USB drives velcro'd to the lid of my Macbook (running Windows), with a Linux VM sharing the ZFS volume via CIFS.
Best Answer
Before all, you need to be sure that the drive is 100% healthy at hardware level.
The first thing I would do is checking the S.M.A.R.T values on a computer running Windows, using a tool like HD Sentinel or equivalent. This will give you a good estimation about in which condition the drive is.
You should test the drive connected in an external USB or eSATA dock as the original drive enclosure may also have problems, like weak electrical contact or so.
Then, I would low level clone the drive to another one. Even if its condition is 100% Ok according to the S.M.A.R.T. values. This step can reveal a few defective sectors, which were not referenced yet by the S.M.A.R.T. monitoring.
Even if your drive is 100% healthy, every serious data recovery professional will tell you than in a situation like the one you're encountering, we never work on the original drive, but always on a clone, especially when possibly dangerous commands like verify/repair ones are used.
The fact that your drive suggests that you should initialize it (-- don't to it ! --) if often an indicator or hardware issues, like corrupted firmware or damaged heads, requiring data recovery by a company that is specialized in data recovery (and not the first local computer shop you can find).