[Electronic M]

An isolation transformer may work, but if the primary and secondary windings start to (or currently) leak current between each other, or you ever forget and run the set without it things still could go wrong.

90% of the time the alignment is good enough as found after paper caps and weak tubes have been changed (clean the tuner contacts before you dismiss the system) that you will be hard pressed to notice a difference between RF and direct injection. Also if the CRT does not focus really well it will look mediocre to bad no matter how good the IF is or how you feed it signal. Ignore direct injection till you get it working.
50's-60's sets are by and large not designed to be as sharp as newer CRT sets so the old gamer/home theater saws about composite being better than RF often don't apply.

IF alignment in TV is much more involved than radio. You have to have an Oscilloscope and a properly calibrated TV Sweep/Marker alignment generator to do an IF alignment (the turn and observe method will only screw it up).

There are no HDMI to RF adapters on the market AFAIK so if you plan to use an HDMI based signal source you will be buying an HDMI to composite video adapter and probably an RF modulator like it or not. Personally I don't know what you would connect that would not use composite or some analog connection. I've got a cable box, DTV box, DVD, VCR, (several older video formats), and a windows 7 PC (for web videos and digital vids in formats my DVD player can't handle) with s-video out on it's video card as analog signal sources...NONE of them have only HDMI (all have analog outputs) and they cover everything programming wise I could imagine watching on a TV and more... So I've never needed an HDMI converter.

If you go RF I recommend getting a Blonder Tongue agile modulator (AM40, AM60, or BAVMz series), they are worlds better signal quality wise than a Radio Shack (or other off the shelf) RF modulator (and can be had for under, sometimes well under, $40). A BT will actually PROPERLY adhere to broadcast specifications (no crude approximations like the cheap crap), and most with an optimal antenna set (ask me for details) and at near max power can send RF wirelessly for 70' to a suburban block with ease...Which can be super handy if you want to move sets around or have them in multiple rooms (I speak from experience) or outdoors. I use all three families of BT mods, for wireless broadcasting and am quite pleased with their performance.

One other thing that is useful to have is a 90's or newer portable or small screen CRT set (can be had for less than $5) to test your signal sources, and if transmitting RF, your reception range.