B&M makes a nice shifter that is a bit shorter than stock, it goes for about 45 bucks or so.

I'm pretty sure that Razo knob of yours is also a bit shorter than stock. Combined, the shifter should be noticeably lower than stock without being too bad.

A little trick for keeping the shift boot flush against the knob is to put a zip tie or washer on the shifter where you want the boot to rest. It will hold the boot right up to the bottom of the knob.