I have MM's C/O for Bilsteins on my 86, with 94/95 spindles, 04 Mach 1 a-arms, MM CC plates and STB, MM bumpsteer kit and 96 Cobra 17x8s running 245/45/17s. The C/Os clear the wheels because (i) I'm using a 10" spring and (ii) I've moved the track out 1.25" per-side wider than the stock 86 (2.5" wider). As you may have read, the 86 and earlier k-members locate the a-arm pickups .5" per-side inboard of the later v8 cars (1" narrower front track). When this narrower k-member/stock a-arm is combinded with the sn95 spindle, you lose negative camber (top of the tire tilts outboard). Sometiimes, you can just correct this negative camber problem with CC plates alone to achieve a stock spec alignmment setting (CC plate is a minimum requirement) but you will probably not get a perforamance alignment setting. In my case, I had to go with the longer sn95 a-arms. Now because of the longer arms, the angle of the strut is just enough to clear the wheels (tower is in the same place; spindle strut mount is moved out which increases strut angle and negative camber). Depending on your wheel choice, you may have clearance problems if you retain the stock k-member and a-arms with your Bilstein C/O; you will have excessive positive camber.
As for the Cobra rear shocks, I also have an 01 Cobra. It's not the weight of the components; it's the elimination of bind. Similar to installing a T/A on a stick axle, there is very little bind in the IRS comperable to the converging 4-link of the standard Mustang. Hince, you need higher spring rates for the IRS (like the T/A) which requires a different damping rate to control them. The IRS shocks are not suitable for a stick axle even with a T/A; certainly not with a stock 4-link (I wish since I have IRS shocks).