I had also a bit of problems when I upgraded my own Jr 6 weeks ago to a older Mint 18lb MK-IV Platter.
yes, with the VPI two piece (conjoined as a one piece) Black Spindle Clamp It would touch the inside of the Cover. Upon doing a bit of thought on solutions, discovered that VPI had placed a Rubber Spindle Washer on top of each Sorbothane Puck, so those were removed, and of course then, the Motor Cover would've contacted the Motor Pulley, so fout thicker Rubber Washers were placed between the Motor Cover, and the three Standoffs, and that solved that.
If the Bearing-bearing Well is the older style, once can slightly lower the Bearing in how it rides in the Bearing Well by Slightly unscrewing the Brass Plug at the bottom of the Bearing Well. Just make sure that there's some clearance between the bottom of the Flange of the bearing (What the Platter rests on) and the upper surface of the Flange of the Bearing Well. Provided there's no contact-rubbing, there's no problem. This also may permit you to achieve an acceptable VTA, without having to have the Tonearm as high.
Now onto Platter fluctuations. Most likely with the heavier Platter, your Platter Belt is no doubt old, stretched, and now has difficulty with the heavier Platter. These only last a year, or so, then are stretched a bit too much to be adequate. Get a new Belt. Make sure you have cleaned, and lubed the Bearing, and Bearing Well contact surfaces with a very fine coat of Oil. Mobil 1 10-30W works fine for this.
I also have no idea which Tonearm you are using, but as we're all aware, yes the taller 4" Dustcover would be one option, and the others depending how much clearance you're lacking may be solved by other fixes.
Generally, the HW-19 came with 4 very thin Cork Pads that sat at each corner of the Turntable Base, which the Dustcover rests upon. These can be removed, and replaced with a thicker pad, and people like McMaster-Carr carry these neat little Bumpers, and can be gotten in a more attractive clear Silicone Bubble Shaped 1/2 round Bumper. This will perhaps give you another 1/8" clearance. The other cheap fix option is to raise the rear of the dustcover by loosening the 2 Hinge Clamps at the rear of the Table, raise the Dustcover off the rear two bumpers by another 3/16", and then tighten the Hinge Clamps back up.
Of course, this may not still cure your problems, or you may feel that they are not sound fixes, and things are still a little bit too close.
This was what I found, and to cure my own Spindle Clamp clearance issues, I went ahead, and had my Machinist friend fabricate a beautiful solid Billet, Polished Aluminum Clamp Puck to my specifications, 9With 1/4"x20 threaded central hole) and it works perfectly, allows plenty of clearance now, and looks beautiful. If anyone wants to see a pic of how this looks, drop me a line privately, I'll shoot off a pic to you.
Since I am using an AQ PT-6 Arm, there were no clearance issues with the Dustcover, but there sure was a lot of Tonearm Mounting Shaft showing due to raising the Arm to achieve proper VTA with the thicker MK-IV Platter.
Again, for a nominal price, my friend Machined a .5" Aluminum Spacer Donut Shim, with three holes for the mounting Screws to Plinth. All I needed then was three longer screws (1-1/4" SS) to button it all back up. Again, an attractive improvement, and it sure looks a lot better than seeing all that exposed Tonearm Shaft, and the ugly previous Allen Set Screw Marks on the Shaft when I had the Jr Platter on board. Mark