Cool, I was afraid you'd already burned them in! For what it's worth, where your shifter currently resides is about where it would reside with the engine in the "Downey approved" location, and the original transmission top cover. You'd just need to bend the shifter a tad to have it clear the heater, which was the standard operating procedure for years on these conversions.
Really, as long as you don't have clearance and fitment issues elsewhere, there's probably nothing outwardly wrong with your location. As I mentioned, my engine was installed even further forward, with SUPER long doglegs in the shifters, but aside from a mile-long shift-throw, it drove and cooled just fine.
With the FJ60 shift tower, I think there's probably a happy medium between where you are, and where you're going. The Downey instructions are based on keeping the original shift tower - it has to be that far back to clear the heater, and even so, requires a bit of a shifter dog-leg and modifications to the tunnel. With the 60-series tower, perhaps you can leave a slightly wider gap at the firewall to improve cooling. You'd just need to confirm clearances elsewhere (steering shaft, balancer on the axle, etc.).
Like I said, if I were to do it again, I believe the "perfect" number would have been 1/4" to 1/2" further forward. The shifter would still probably fit in the stock hole (albeit off-center) with the 60-series tower, I'd have a touch more clearance between engine and firewall, and my driveshafts would be the exact same length. It was just too "nit-picky" a reason to cut everything out and weld it back in.