Do persevere with the SPI and Arduino. Its a skill that's worth cracking because it opens up the use of so many clever chips that can save you much money and effort building complex circuits. However to get your VFD clocks going can be done in pure logic + those Micrel High side drivers, and I think I agree you'll get more satisfaction that way.
I suggest you make it modular so you can 'borrow' the VFD as a complete subassembly for other projects - put the MIC2981 chips, the +HT boost circuit, the filament supply and the VFD all on one board with a pin header for all the segment and digit control lines to the MIC2981 chips. IIRC your VFD had 21 grid and anode pins so that lot would fit nicely on a 34 pin or 40 pin 2 row box header you could cannibalise old floppy or IDE cables to make mating cables for, leaving enough pins for plenty of grounds and 5V pins. (As a rule of thumb: Use twice as many ground pins as 5v pins.) If you connect a 'bare' pizeo sounder disk to a spare MIC2981 output, with a lower value pulldown - say 33K, you could use it as a fairly loud beeper for an alarm. Just gate a squarewave audio tone.
e.g. to do it in pure logic, 1.024KHz from your '4060 divider chain ANDed with the 2Hz final output of the '4060 to get a 'beep-beep-beep' effect and also with the output of your alarm latch which would be triggered by your alarm time match circuit. The easiest way of entering the alarm time would be to decode each digit to individual output pins and use rotary switches or jumper wires to program it. Hours >=24 = alarm off. The selected digit pins would all be ANDed together and applied to the set input of your alarm latch, with the reset input connected to a pushbutton.