The AutoStick uses a compact clutch inside (quite expensive to replace). In normal usage it doesn't take much of a beating since the torque converter handles most of the engagement shock, but its engagement speed must be modulated by the vacuum bleedoff rate of the control solenoid.
The stock carburetor provides a vacuum signal to the solenoid so that engagement is gentle/slow under light loads but rapid (to limit slippage) when accelerating hard.
Without that signal, engagement tends to be harsh - particularly when you first release the shifter when taking off from a standing start. If the control valve is adjusted to allow going into Reverse without a big clunk, engagement will be slow under all conditions which increases wear on the clutch significantly.
Better IMO to leave the control valve adjustment alone, and rig a momentary bypass for the neutral safety switch which will allow starting the engine in gear so that the transmission mounts will last longer.
With stock heads and heat exchangers, keeping the displacement in the 1700cc range and selecting a mild cam would be wise in my opinion. 88x69 would be the easiest/least expensive way to go; with the strokers you'll encounter issues (engine width, pushrod length, possible need for internal clearancing) that won't come up with the stock stroke. 1775cc (90.5x69) is a little bit bigger than I'd recommend, but should give you torque comparable to that of 85.5x76 with fewer assembly hassles.
Get a nice valvejob done, and install steel shims under the valvesprings. Mild intake port work is worth doing; at minimum make sure that the manifolds & heads are port-matched.
With the AutoStick oil pump it's possible to add a full-flow filter, but it's trickier to do since you have to drill & tap the case for both the "out" and "in" lines. Without welding additional material to the case it's potentially a weak point...and #4 main bearing still receives unfiltered oil:
http://images.thesamba.com/vw/gallery/pix/802206.jpg
The stock "doghouse" cooler setup is hard to beat and is all that most engines will ever need - switching to an external cooler solely for the purpose of adding an inline filter isn't a very good idea. The filter won't be a true "full-flow", either, since it'll be bypassed during engine warmup (when most wear particles are generated).
One possible way to plumb a full-flow filter would be by using an aftermarket return fitting which goes into the oil-pump-end pressure control valve bore, and taking the "dirty" oil out through a fitting at the point which is normally used for the return - this arrangement would require that a plug be installed inside that passage. #4 main still doesn't get filtered oil, and the pressure control valve is eliminated which will slow oil warmup some. This fitting:
http://www.machine7.com/product.php?xProd=13163
One other option would be to install an aftermarket sump with provision for a pickup-side filter element, like Citroen 2CV's use....I'm not a proponent of this setup, but I suppose it could work if maintained regularly:
http://www.cbperformance.com/ProductDet ... tCode=1709
All things considered, for this application I'd probably forego adding any filter - millions of VWs have managed without one for many years. Use a magnetic drainplug, or just epoxy a strong magnet to the bottom of the sump plate, to catch ferrous particles.
A "bypass" type filter (Frantz, for example) could also be used, but in my experience they're prone to reducing hot-idle oil pressure to unacceptable levels unless used with a higher-volume pump, not an option for the AutoStick.
