Went through a more difficult than expected cam install in my 2005 GT myself earlier this year, I feel your pain.
First, check for codes and make sure that Bama has all the correct information for your tune. Their tune is not going to be great by any means but it should at least run. My tune from them for my Hot Rod Cams is just "tolerable" at best, I plan to switch to Lito or Lund in the near future.
Second, if you have any doubt at all that the timing jumped a tooth, the front cover needs to come off and timing needs to be checked. I highly encourage getting rid of or returning the aftermarket phasers and going with a complete genuine FRPP timing kit, especially since you have a 2005. There have been updates to the phasers and tensioners since 2005 that are worth going that route for. Steve@Tasca is a vendor on this forum and will beat anybody's prices on it. Find the Ford Service Manual and follow the instructions to a "T" for disassembly and reassembly, label every bolt and part that comes off, and use correct torque sequences/values. Make sure all electrical plugs get plugged back in to the right connectors. Pay very special attention to the part numbers making sure that everything goes in the correct place. Tensioners and the tensioner arms look VERY similar but there are "lefts" and "rights", so double and triple check. The two idler pulleys on the front cover also look nearly identical and are the same way. Most importantly, make sure that all the timing marks are lined up correctly. It is a straightforward process but takes attention to detail. It's not necessary, but I even went so far on mine as to drop the oil pan and replace the gasket to make sure I got a good seal and no leaks. I also like Permatex "Right Stuff" over the usual Ultra Black RTV, just find it to be more user friendly.
It's also a good idea to "prime" the engine before you start it if you do all of that. It will help make sure the tensioners are pressurized so that you don't jump a tooth when you start it for the first time. There are multiple ways to go about priming it. Others I'm sure will disagree, but I think the easiest way is to fill it up with oil with the valve covers off, and then turn the engine over BY HAND until you can see the timing chains have no slack and that the valve train is getting lubricated.
While you have the front cover off, it's also a great time to upgrade to the 2013+ GT500 oil pump with billet backplate. Swap the pressure relief spring over from your OEM pump to keep the proper oil pressure. There are threads on this forum about this if you do a search. For less than $100 it's great insurance while you're already that far into the motor.
Also would be a good time to upgrade to the 2007+ coolant crossover and hose setup if you're interested. It doesn't do anything for performance but it sure makes the engine bay look nicer and frees up some space. Could also powder coat your timing cover to make it look a little nicer if you wanted.
Good luck.
