1. Use the newest of your Accushift RD's. Each has a two character date code stamped on the back. Date them at Vintage-trek.com. The 1988 and onwards design has an improved pulley pivot design that Suntour and Shimano fought over for years in patent court. It really helps indexing.

2. Use a NEW chain. Modern SRAM PC-850 chains ($12 at jensonusa.com) work fine.

3. For best results, the center to center distance of the rear axle to the RD mounting bolt MUST be within 24-28mm. You can flex up to 30mm. Beyond 30mm indexing goes to hell in a hand basket. With horizontal dropouts, you can often slide the rear wheel adequately forward to achieve the proper distance.

4. Use an Accushift (i.e. four slot removal tool) seven cog freewheel, because seven speed Accushift spacing is different than Shimano spacing:
--Accushift seven speed spacing center to center from the smallest cog inwards to the largest cog is 5.3mm, 5.3mm, 4.8mm/4.8/4.8/4.8/4.8mm,
--Shimano is a uniform 5.0mm across the cluster.

5. Use modern compressionless shift cable housing. An absolute must. MUST. No exceptions. Note that the rear loop of cable housing from the chainstay stop into the RD tension adjuster bolt / stop is shorter for Accushift than for Shimano because Accushift RD springs are far stronger than Shimano 'SLR' springs. Rear loop cable housing length should be 30cm (just shy of 1'), no longer.

6. Alpha and Alpha 2000 RD's and shifters are NOT compatible with other Acchushift components, only with other Alpha components.

7. Yellowjersey.org has a 30 page Suntour Accushift Tech manual you can download.

8. Be sure to adjust the RD 'B' screw properly. Adjust the RD High / Low stops. Adjust the front derailer High / Low stops. Once those adjustments have been made, put the chain on the largest rear cog/smallest front ring and then adjust the RD B screw so that 1-1/2 chain links separate the largest rear cog from the upper RD pulley.

I have several sets of Command Shifters running--you might say they were made for me. If you decide to go in another direction, perhaps you could PM me with regards to the future of yours.