Noun or phrase similar to clone with positive connotation?

The word analogue lacks a negative connotation and appears to convey your intended meaning well.

In your example sentences:

"...released the Tintium line of microprocessors, an analogue of Intel's Pentium line."

"...sought the services of Biocraft LLC, who custom designed and attached a prosthetic analogue of his original limb."

The word you're looking for is emulate.

emulate.
ˈɛmjʊleɪt/
verb. 1. match or surpass (a person or achievement), typically by imitation.
"most rulers wished to emulate Alexander the Great"
"hers is not a hairstyle I wish to emulate"
COMPUTING
2. reproduce the function or action of (a different computer, software system, etc.).
"the adaptor is factory set to emulate a Hercules graphics board"

Adapted from Google's definition

If what you want it as a noun, then I'd go with: emulation or even, emulator

It certainly connotes a desire to be similar in a positive sense, out of awe or respect.

Consider a drop-in replacement.