Quick question, still really new to jailbreaking.
If I jailbreak now, just to look around and see what this is all about, will I have to re-jailbreak when Mobile Substrate is updated? Or is that pushed through a Cydia update?
Nope, it's pushed through Cydia. MobileSubstrate is a package in Cydia. When Saurik updates the current version with a newer version, an update will appear in Cydia that allows you to upgrade the version you're currently running. No re-jailbreaking required.
Bootstrap has worked pretty well for me as Willerz outlined - but it's a little weird and occasionally resprings or reboots on its own -- making you think something else could be wrong. It's not. But there's a new tweak out called MS Cache Fix that does what Bootstrap does - a little more elegantly from what I'm reading. I forget the repo where to get it - and haven't tried myself yet. But what I'm reading is very positive and makes those of using 4, 4S and 5 have a little more success with tweaks based on Mobile Substrate. Right now, with BootStrap, I'm using Gridlock and even Winterboard pretty successfully. There's only one theme out there certified iOS7 ready.. and it's okay so far.. iFile's fine too. All of this on my 4 and 4S.
Heading out to get my Christmas present of a 5S today! Yay!
You may be referring to MS Reload Fix from the http://devbug.me/apt/ repo.
I use my phone for my work e-mail... Exchange specifically and it locks my ability to turn off the passcode unless I ditch the e-mail account. I'm guessing I should do all that since this appears to have a full reboot of the phone involved... is this a recommended or required thing... i.e. no passcode?
It's recommended to the point where it's almost required, because if it fails consecutively several times, you may end up with overlapping and corrupted cache files, which will require a restore of your device prior to jailbreaking. Reason is that it's difficult (if not impossible) to make changes to a locked device, much like how you can't perform a simple restore of a device with a passcode on it by clicking on the Restore button in iTunes.