429 Thunderjet into 68 fastback

First of all, what year is your TJ and have you pulled any castings from it yet? Do you have a C9, D1VE or D0VE block? What heads do you have, D3 or D0VE? 429's in particular are prone to piston skirt cracking, which leads to moderate cylinder wall damage, I would suggest inspecting the shortblock before going forward. I am going to assume that you have D0VE heads, if this is the case, you have a few more options.

To answer your first question, yes you can run a power booster with a 429/460 variant engine, however it depends on your swap combination and motor mounts. There are a lot of companies out there that make swap kits now, you can find them by doing a quick google search. Probably the most reputable company right now is http://www.critesrestoration.com/. A couple benefits of their mounts is that if will raise and pull your engine forward about 1", giving added clearance for a powerbooster, and header to crossmember clearance. They also recently came out with their Generation II headers which I'd strongly recommend. You can also find headers from FPA (shorty), D&D, and MPG head service. Another option is to go on summit and purchase flanges which then you can have custom headers made at an exhaust shop.

You will also need to consider your suspension, a SB swaybar will hug the oil pan, Mustangs Unlimited sells a sway bar designed for a bigblock, it has a different curve to it for added clearance. Springs you have more options than a SB, but a good option would be a 600# designed for a 351 range SB, it will give you a 1" drop with better handling.

Transmissions you have even more options. The cheapest option will be a C6 transmission, you will most likely not need to rebuild it, however it's never a bad idea not to. You CAN run a C4 transmission, however it will need to be built and you will need the correct bellhousing, this a more expensive option. You also have the option of running an AOD with a bellhousing correct for a 429/460/351M/400 variant. You also have the option of a powerglide, but it will cost about the same as a C4. Of course, you will need the correct flexplate, starter and torque convertor for these applications depending on your transmission choice. You have choices on transmission crossmembers, you will find all but the AOD and powerglide crossmember at any vendor, you will most likely have to use either a swap or a universal crossmember. You will be fine with a 2500 stall would be fine on the street. You can bump it up to 3000 if you'd like some infrequent track runs.

You have so many engine options, it's going to be up to you how much you power you want. Are you planning on keeping the stock 429 stroke? You can always get a 460 crank and pistons and up the ci to a 460".

Now, assuming that you have D0VE heads, these are still good heads and have potentional, these heads can become very stout when you port them, install new valves, mill them down to 72cc, etc. This would be my first option for budget, next would be a pair of A429 or A460 heads, which also can be ported. An Edelbrock Victor intake, matched would be a good combo with these heads. Holley 850-900, and I would call a cam manufacturer for suggestions or get a custom grind depending on your configuration in the end.

That should give you enough power to merge into traffic.